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IMP Reference Guide  develop.50fdd7fa33,2025/08/31
The Integrative Modeling Platform
bff/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.3.1
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2025 IMP Inventors. All rights reserved.
10 
11 
12 
13 
14 from sys import version_info as _swig_python_version_info
15 import _IMP_bff
16 
17 try:
18  import builtins as __builtin__
19 except ImportError:
20  import __builtin__
21 
22 def _swig_repr(self):
23  try:
24  strthis = "proxy of " + self.this.__repr__()
25  except __builtin__.Exception:
26  strthis = ""
27  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
28 
29 
30 def _swig_setattr_nondynamic_instance_variable(set):
31  def set_instance_attr(self, name, value):
32  if name == "this":
33  set(self, name, value)
34  elif name == "thisown":
35  self.this.own(value)
36  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
37  set(self, name, value)
38  else:
39  raise AttributeError("You cannot add instance attributes to %s" % self)
40  return set_instance_attr
41 
42 
43 def _swig_setattr_nondynamic_class_variable(set):
44  def set_class_attr(cls, name, value):
45  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
46  set(cls, name, value)
47  else:
48  raise AttributeError("You cannot add class attributes to %s" % cls)
49  return set_class_attr
50 
51 
52 def _swig_add_metaclass(metaclass):
53  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
54  def wrapper(cls):
55  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
56  return wrapper
57 
58 
59 class _SwigNonDynamicMeta(type):
60  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
61  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
62 
63 
64 import weakref
65 
66 class IMP_BFF_SwigPyIterator(object):
67  r"""Proxy of C++ swig::IMP_BFF_SwigPyIterator class."""
68 
69  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
70 
71  def __init__(self, *args, **kwargs):
72  raise AttributeError("No constructor defined - class is abstract")
73  __repr__ = _swig_repr
74  __swig_destroy__ = _IMP_bff.delete_IMP_BFF_SwigPyIterator
75 
76  def value(self):
77  r"""value(IMP_BFF_SwigPyIterator self) -> PyObject *"""
78  return _IMP_bff.IMP_BFF_SwigPyIterator_value(self)
79 
80  def incr(self, n=1):
81  r"""incr(IMP_BFF_SwigPyIterator self, size_t n=1) -> IMP_BFF_SwigPyIterator"""
82  return _IMP_bff.IMP_BFF_SwigPyIterator_incr(self, n)
83 
84  def decr(self, n=1):
85  r"""decr(IMP_BFF_SwigPyIterator self, size_t n=1) -> IMP_BFF_SwigPyIterator"""
86  return _IMP_bff.IMP_BFF_SwigPyIterator_decr(self, n)
87 
88  def distance(self, x):
89  r"""distance(IMP_BFF_SwigPyIterator self, IMP_BFF_SwigPyIterator x) -> ptrdiff_t"""
90  return _IMP_bff.IMP_BFF_SwigPyIterator_distance(self, x)
91 
92  def equal(self, x):
93  r"""equal(IMP_BFF_SwigPyIterator self, IMP_BFF_SwigPyIterator x) -> bool"""
94  return _IMP_bff.IMP_BFF_SwigPyIterator_equal(self, x)
95 
96  def copy(self):
97  r"""copy(IMP_BFF_SwigPyIterator self) -> IMP_BFF_SwigPyIterator"""
98  return _IMP_bff.IMP_BFF_SwigPyIterator_copy(self)
99 
100  def next(self):
101  r"""next(IMP_BFF_SwigPyIterator self) -> PyObject *"""
102  return _IMP_bff.IMP_BFF_SwigPyIterator_next(self)
103 
104  def __next__(self):
105  r"""__next__(IMP_BFF_SwigPyIterator self) -> PyObject *"""
106  return _IMP_bff.IMP_BFF_SwigPyIterator___next__(self)
107 
108  def previous(self):
109  r"""previous(IMP_BFF_SwigPyIterator self) -> PyObject *"""
110  return _IMP_bff.IMP_BFF_SwigPyIterator_previous(self)
111 
112  def advance(self, n):
113  r"""advance(IMP_BFF_SwigPyIterator self, ptrdiff_t n) -> IMP_BFF_SwigPyIterator"""
114  return _IMP_bff.IMP_BFF_SwigPyIterator_advance(self, n)
115 
116  def __eq__(self, x):
117  r"""__eq__(IMP_BFF_SwigPyIterator self, IMP_BFF_SwigPyIterator x) -> bool"""
118  return _IMP_bff.IMP_BFF_SwigPyIterator___eq__(self, x)
119 
120  def __ne__(self, x):
121  r"""__ne__(IMP_BFF_SwigPyIterator self, IMP_BFF_SwigPyIterator x) -> bool"""
122  return _IMP_bff.IMP_BFF_SwigPyIterator___ne__(self, x)
123 
124  def __iadd__(self, n):
125  r"""__iadd__(IMP_BFF_SwigPyIterator self, ptrdiff_t n) -> IMP_BFF_SwigPyIterator"""
126  return _IMP_bff.IMP_BFF_SwigPyIterator___iadd__(self, n)
127 
128  def __isub__(self, n):
129  r"""__isub__(IMP_BFF_SwigPyIterator self, ptrdiff_t n) -> IMP_BFF_SwigPyIterator"""
130  return _IMP_bff.IMP_BFF_SwigPyIterator___isub__(self, n)
131 
132  def __add__(self, n):
133  r"""__add__(IMP_BFF_SwigPyIterator self, ptrdiff_t n) -> IMP_BFF_SwigPyIterator"""
134  return _IMP_bff.IMP_BFF_SwigPyIterator___add__(self, n)
135 
136  def __sub__(self, *args):
137  r"""
138  __sub__(IMP_BFF_SwigPyIterator self, ptrdiff_t n) -> IMP_BFF_SwigPyIterator
139  __sub__(IMP_BFF_SwigPyIterator self, IMP_BFF_SwigPyIterator x) -> ptrdiff_t
140  """
141  return _IMP_bff.IMP_BFF_SwigPyIterator___sub__(self, *args)
142  def __iter__(self):
143  return self
144 
145 # Register IMP_BFF_SwigPyIterator in _IMP_bff:
146 _IMP_bff.IMP_BFF_SwigPyIterator_swigregister(IMP_BFF_SwigPyIterator)
147 
148 _value_types=[]
149 _object_types=[]
150 _raii_types=[]
151 _plural_types=[]
152 
153 IMP_DEBUG = _IMP_bff.IMP_DEBUG
154 
155 IMP_RELEASE = _IMP_bff.IMP_RELEASE
156 
157 IMP_SILENT = _IMP_bff.IMP_SILENT
158 
159 IMP_PROGRESS = _IMP_bff.IMP_PROGRESS
160 
161 IMP_TERSE = _IMP_bff.IMP_TERSE
162 
163 IMP_VERBOSE = _IMP_bff.IMP_VERBOSE
164 
165 IMP_MEMORY = _IMP_bff.IMP_MEMORY
166 
167 IMP_NONE = _IMP_bff.IMP_NONE
168 
169 IMP_USAGE = _IMP_bff.IMP_USAGE
170 
171 IMP_INTERNAL = _IMP_bff.IMP_INTERNAL
172 
173 IMP_KERNEL_HAS_LOG4CXX = _IMP_bff.IMP_KERNEL_HAS_LOG4CXX
174 
175 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_bff.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
176 
177 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_bff.IMP_COMPILER_HAS_DEBUG_VECTOR
178 
179 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_bff.IMP_COMPILER_HAS_RANDOM_SHUFFLE
180 
181 IMP_COMPILER_HAS_THREE_WAY = _IMP_bff.IMP_COMPILER_HAS_THREE_WAY
182 
183 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_bff.IMP_KERNEL_HAS_BOOST_RANDOM
184 
185 IMP_KERNEL_HAS_NUMPY = _IMP_bff.IMP_KERNEL_HAS_NUMPY
186 
187 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_bff.IMP_KERNEL_HAS_BOOST_SYSTEM
188 
189 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_bff.IMP_KERNEL_HAS_GPERFTOOLS
190 
191 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_bff.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 
193 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_bff.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 
195 IMPKERNEL_SHOW_WARNINGS = _IMP_bff.IMPKERNEL_SHOW_WARNINGS
196 
197 
198 import sys
199 class _DirectorObjects:
200  """@internal Simple class to keep references to director objects
201  to prevent premature deletion."""
202  def __init__(self):
203  self._objects = []
204  def register(self, obj):
205  """Take a reference to a director object; will only work for
206  refcounted C++ classes"""
207  if hasattr(obj, 'get_ref_count'):
208  self._objects.append(obj)
209  def cleanup(self):
210  """Only drop our reference and allow cleanup by Python if no other
211  Python references exist (we hold 3 references: one in self._objects,
212  one in x, and one in the argument list for getrefcount) *and* no
213  other C++ references exist (the Python object always holds one)"""
214  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
215  or x.get_ref_count() > 1]
216 # Do in two steps so the references are kept until the end of the
217 # function (deleting references may trigger a fresh call to this method)
218  self._objects = objs
219  def get_object_count(self):
220  """Get number of director objects (useful for testing only)"""
221  return len(self._objects)
222 _director_objects = _DirectorObjects()
223 
224 class _ostream(object):
225  r"""Proxy of C++ std::ostream class."""
226 
227  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
228 
229  def __init__(self, *args, **kwargs):
230  raise AttributeError("No constructor defined")
231  __repr__ = _swig_repr
232 
233  def write(self, osa_buf):
234  r"""write(_ostream self, char const * osa_buf)"""
235  return _IMP_bff._ostream_write(self, osa_buf)
236 
237 # Register _ostream in _IMP_bff:
238 _IMP_bff._ostream_swigregister(_ostream)
239 IMP_C_OPEN_BINARY = _IMP_bff.IMP_C_OPEN_BINARY
240 
241 import IMP
242 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 
244 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 
246 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_bff.IMP_CGAL_HAS_BOOST_RANDOM
247 
248 IMP_CGAL_HAS_NUMPY = _IMP_bff.IMP_CGAL_HAS_NUMPY
249 
250 IMPCGAL_SHOW_WARNINGS = _IMP_bff.IMPCGAL_SHOW_WARNINGS
251 
252 import IMP.cgal
253 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_bff.IMP_ALGEBRA_HAS_IMP_CGAL
254 
255 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
256 
257 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
258 
259 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_bff.IMP_ALGEBRA_HAS_BOOST_RANDOM
260 
261 IMP_ALGEBRA_HAS_CGAL = _IMP_bff.IMP_ALGEBRA_HAS_CGAL
262 
263 IMP_ALGEBRA_HAS_NUMPY = _IMP_bff.IMP_ALGEBRA_HAS_NUMPY
264 
265 IMP_ALGEBRA_HAS_ANN = _IMP_bff.IMP_ALGEBRA_HAS_ANN
266 
267 IMPALGEBRA_SHOW_WARNINGS = _IMP_bff.IMPALGEBRA_SHOW_WARNINGS
268 
269 import IMP.algebra
270 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_bff.IMP_DISPLAY_HAS_IMP_CGAL
271 
272 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
273 
274 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
275 
276 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_bff.IMP_DISPLAY_HAS_BOOST_RANDOM
277 
278 IMP_DISPLAY_HAS_CGAL = _IMP_bff.IMP_DISPLAY_HAS_CGAL
279 
280 IMP_DISPLAY_HAS_NUMPY = _IMP_bff.IMP_DISPLAY_HAS_NUMPY
281 
282 IMPDISPLAY_SHOW_WARNINGS = _IMP_bff.IMPDISPLAY_SHOW_WARNINGS
283 
284 import IMP.display
285 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
286 
287 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
288 
289 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
290 
291 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
292 
293 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_CGAL
294 
295 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_HDF5
296 
297 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_bff.IMP_SCORE_FUNCTOR_HAS_NUMPY
298 
299 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_bff.IMPSCOREFUNCTOR_SHOW_WARNINGS
300 
301 import IMP.score_functor
302 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_bff.IMP_STATISTICS_HAS_IMP_CGAL
303 
304 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
305 
306 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
307 
308 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_bff.IMP_STATISTICS_HAS_BOOST_RANDOM
309 
310 IMP_STATISTICS_HAS_CGAL = _IMP_bff.IMP_STATISTICS_HAS_CGAL
311 
312 IMP_STATISTICS_HAS_NUMPY = _IMP_bff.IMP_STATISTICS_HAS_NUMPY
313 
314 IMPSTATISTICS_SHOW_WARNINGS = _IMP_bff.IMPSTATISTICS_SHOW_WARNINGS
315 
316 import IMP.statistics
317 IMP_CORE_HAS_IMP_CGAL = _IMP_bff.IMP_CORE_HAS_IMP_CGAL
318 
319 IMP_CORE_HAS_IMP_KERNEL = _IMP_bff.IMP_CORE_HAS_IMP_KERNEL
320 
321 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_CORE_HAS_BOOST_FILESYSTEM
322 
323 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
324 
325 IMP_CORE_HAS_BOOST_RANDOM = _IMP_bff.IMP_CORE_HAS_BOOST_RANDOM
326 
327 IMP_CORE_HAS_CGAL = _IMP_bff.IMP_CORE_HAS_CGAL
328 
329 IMP_CORE_HAS_HDF5 = _IMP_bff.IMP_CORE_HAS_HDF5
330 
331 IMP_CORE_HAS_NUMPY = _IMP_bff.IMP_CORE_HAS_NUMPY
332 
333 IMPCORE_SHOW_WARNINGS = _IMP_bff.IMPCORE_SHOW_WARNINGS
334 
335 import IMP.core
336 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_bff.IMP_CONTAINER_HAS_IMP_ALGEBRA
337 
338 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_bff.IMP_CONTAINER_HAS_IMP_CGAL
339 
340 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_bff.IMP_CONTAINER_HAS_IMP_DISPLAY
341 
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_bff.IMP_CONTAINER_HAS_IMP_KERNEL
343 
344 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_bff.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
345 
346 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
347 
348 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
349 
350 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_bff.IMP_CONTAINER_HAS_BOOST_RANDOM
351 
352 IMP_CONTAINER_HAS_CGAL = _IMP_bff.IMP_CONTAINER_HAS_CGAL
353 
354 IMP_CONTAINER_HAS_HDF5 = _IMP_bff.IMP_CONTAINER_HAS_HDF5
355 
356 IMP_CONTAINER_HAS_NUMPY = _IMP_bff.IMP_CONTAINER_HAS_NUMPY
357 
358 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_bff.IMP_CONTAINER_HAS_PYTHON_IHM
359 
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_bff.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 
362 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_bff.IMP_CONTAINER_HAS_ROBIN_MAP
363 
364 IMPCONTAINER_SHOW_WARNINGS = _IMP_bff.IMPCONTAINER_SHOW_WARNINGS
365 
366 import IMP.container
367 IMP_ATOM_HAS_IMP_CGAL = _IMP_bff.IMP_ATOM_HAS_IMP_CGAL
368 
369 IMP_ATOM_HAS_IMP_KERNEL = _IMP_bff.IMP_ATOM_HAS_IMP_KERNEL
370 
371 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_bff.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
372 
373 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
374 
375 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_bff.IMP_ATOM_HAS_BOOST_RANDOM
376 
377 IMP_ATOM_HAS_BOOST_REGEX = _IMP_bff.IMP_ATOM_HAS_BOOST_REGEX
378 
379 IMP_ATOM_HAS_CGAL = _IMP_bff.IMP_ATOM_HAS_CGAL
380 
381 IMP_ATOM_HAS_HDF5 = _IMP_bff.IMP_ATOM_HAS_HDF5
382 
383 IMP_ATOM_HAS_NUMPY = _IMP_bff.IMP_ATOM_HAS_NUMPY
384 
385 IMP_ATOM_HAS_PYTHON_IHM = _IMP_bff.IMP_ATOM_HAS_PYTHON_IHM
386 
387 IMPATOM_SHOW_WARNINGS = _IMP_bff.IMPATOM_SHOW_WARNINGS
388 
389 IMP_ATOM_TYPE_INDEX = _IMP_bff.IMP_ATOM_TYPE_INDEX
390 
391 IMP_RESIDUE_TYPE_INDEX = _IMP_bff.IMP_RESIDUE_TYPE_INDEX
392 
393 IMP_HIERARCHY_TYPE_INDEX = _IMP_bff.IMP_HIERARCHY_TYPE_INDEX
394 
395 IMP_CHAIN_TYPE_INDEX = _IMP_bff.IMP_CHAIN_TYPE_INDEX
396 
397 import IMP.atom
398 IMP_EM_HAS_IMP_CGAL = _IMP_bff.IMP_EM_HAS_IMP_CGAL
399 
400 IMP_EM_HAS_IMP_CONTAINER = _IMP_bff.IMP_EM_HAS_IMP_CONTAINER
401 
402 IMP_EM_HAS_IMP_DISPLAY = _IMP_bff.IMP_EM_HAS_IMP_DISPLAY
403 
404 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_bff.IMP_EM_HAS_IMP_SCORE_FUNCTOR
405 
406 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_EM_HAS_BOOST_FILESYSTEM
407 
408 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
409 
410 IMP_EM_HAS_BOOST_RANDOM = _IMP_bff.IMP_EM_HAS_BOOST_RANDOM
411 
412 IMP_EM_HAS_BOOST_REGEX = _IMP_bff.IMP_EM_HAS_BOOST_REGEX
413 
414 IMP_EM_HAS_CGAL = _IMP_bff.IMP_EM_HAS_CGAL
415 
416 IMP_EM_HAS_HDF5 = _IMP_bff.IMP_EM_HAS_HDF5
417 
418 IMP_EM_HAS_NUMPY = _IMP_bff.IMP_EM_HAS_NUMPY
419 
420 IMP_EM_HAS_PYTHON_IHM = _IMP_bff.IMP_EM_HAS_PYTHON_IHM
421 
422 IMPEM_SHOW_WARNINGS = _IMP_bff.IMPEM_SHOW_WARNINGS
423 
424 import IMP.em
425 IMP_BFF_HAS_IMP_ALGEBRA = _IMP_bff.IMP_BFF_HAS_IMP_ALGEBRA
426 
427 IMP_BFF_HAS_IMP_CGAL = _IMP_bff.IMP_BFF_HAS_IMP_CGAL
428 
429 IMP_BFF_HAS_IMP_DISPLAY = _IMP_bff.IMP_BFF_HAS_IMP_DISPLAY
430 
431 IMP_BFF_HAS_IMP_KERNEL = _IMP_bff.IMP_BFF_HAS_IMP_KERNEL
432 
433 IMP_BFF_HAS_IMP_SCORE_FUNCTOR = _IMP_bff.IMP_BFF_HAS_IMP_SCORE_FUNCTOR
434 
435 IMP_BFF_HAS_IMP_STATISTICS = _IMP_bff.IMP_BFF_HAS_IMP_STATISTICS
436 
437 IMP_BFF_HAS_BOOST_FILESYSTEM = _IMP_bff.IMP_BFF_HAS_BOOST_FILESYSTEM
438 
439 IMP_BFF_HAS_BOOST_PROGRAMOPTIONS = _IMP_bff.IMP_BFF_HAS_BOOST_PROGRAMOPTIONS
440 
441 IMP_BFF_HAS_BOOST_RANDOM = _IMP_bff.IMP_BFF_HAS_BOOST_RANDOM
442 
443 IMP_BFF_HAS_BOOST_REGEX = _IMP_bff.IMP_BFF_HAS_BOOST_REGEX
444 
445 IMP_BFF_HAS_CGAL = _IMP_bff.IMP_BFF_HAS_CGAL
446 
447 IMP_BFF_HAS_HDF5 = _IMP_bff.IMP_BFF_HAS_HDF5
448 
449 IMP_BFF_HAS_PYTHON_IHM = _IMP_bff.IMP_BFF_HAS_PYTHON_IHM
450 
451 IMP_BFF_HAS_AVX = _IMP_bff.IMP_BFF_HAS_AVX
452 
453 IMPBFF_SHOW_WARNINGS = _IMP_bff.IMPBFF_SHOW_WARNINGS
454 
455 
456 import numpy as np
457 
458 SHARED_PTR_DISOWN = _IMP_bff.SHARED_PTR_DISOWN
459 
460 class PairFloatFloat(object):
461  r"""Proxy of C++ std::pair< float,float > class."""
462 
463  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
464  __repr__ = _swig_repr
465 
466  def __init__(self, *args):
467  r"""
468  __init__(PairFloatFloat self) -> PairFloatFloat
469  __init__(PairFloatFloat self, float first, float second) -> PairFloatFloat
470  __init__(PairFloatFloat self, PairFloatFloat other) -> PairFloatFloat
471  """
472  _IMP_bff.PairFloatFloat_swiginit(self, _IMP_bff.new_PairFloatFloat(*args))
473  first = property(_IMP_bff.PairFloatFloat_first_get, _IMP_bff.PairFloatFloat_first_set, doc=r"""first : float""")
474  second = property(_IMP_bff.PairFloatFloat_second_get, _IMP_bff.PairFloatFloat_second_set, doc=r"""second : float""")
475  def __len__(self):
476  return 2
477  def __repr__(self):
478  return str((self.first, self.second))
479  def __getitem__(self, index):
480  if not (index % 2):
481  return self.first
482  else:
483  return self.second
484  def __setitem__(self, index, val):
485  if not (index % 2):
486  self.first = val
487  else:
488  self.second = val
489  __swig_destroy__ = _IMP_bff.delete_PairFloatFloat
490 
491 # Register PairFloatFloat in _IMP_bff:
492 _IMP_bff.PairFloatFloat_swigregister(PairFloatFloat)
493 class VectorString(object):
494  r"""Proxy of C++ std::vector< std::string > class."""
495 
496  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
497  __repr__ = _swig_repr
498 
499  def iterator(self):
500  r"""iterator(VectorString self) -> IMP_BFF_SwigPyIterator"""
501  return _IMP_bff.VectorString_iterator(self)
502  def __iter__(self):
503  return self.iterator()
504 
505  def __nonzero__(self):
506  r"""__nonzero__(VectorString self) -> bool"""
507  return _IMP_bff.VectorString___nonzero__(self)
508 
509  def __bool__(self):
510  r"""__bool__(VectorString self) -> bool"""
511  return _IMP_bff.VectorString___bool__(self)
512 
513  def __len__(self):
514  r"""__len__(VectorString self) -> std::vector< std::string >::size_type"""
515  return _IMP_bff.VectorString___len__(self)
516 
517  def __getslice__(self, i, j):
518  r"""__getslice__(VectorString self, std::vector< std::string >::difference_type i, std::vector< std::string >::difference_type j) -> VectorString"""
519  return _IMP_bff.VectorString___getslice__(self, i, j)
520 
521  def __setslice__(self, *args):
522  r"""
523  __setslice__(VectorString self, std::vector< std::string >::difference_type i, std::vector< std::string >::difference_type j)
524  __setslice__(VectorString self, std::vector< std::string >::difference_type i, std::vector< std::string >::difference_type j, VectorString v)
525  """
526  return _IMP_bff.VectorString___setslice__(self, *args)
527 
528  def __delslice__(self, i, j):
529  r"""__delslice__(VectorString self, std::vector< std::string >::difference_type i, std::vector< std::string >::difference_type j)"""
530  return _IMP_bff.VectorString___delslice__(self, i, j)
531 
532  def __delitem__(self, *args):
533  r"""
534  __delitem__(VectorString self, std::vector< std::string >::difference_type i)
535  __delitem__(VectorString self, SWIGPY_SLICEOBJECT * slice)
536  """
537  return _IMP_bff.VectorString___delitem__(self, *args)
538 
539  def __getitem__(self, *args):
540  r"""
541  __getitem__(VectorString self, SWIGPY_SLICEOBJECT * slice) -> VectorString
542  __getitem__(VectorString self, std::vector< std::string >::difference_type i) -> std::vector< std::string >::value_type const &
543  """
544  return _IMP_bff.VectorString___getitem__(self, *args)
545 
546  def __setitem__(self, *args):
547  r"""
548  __setitem__(VectorString self, SWIGPY_SLICEOBJECT * slice, VectorString v)
549  __setitem__(VectorString self, SWIGPY_SLICEOBJECT * slice)
550  __setitem__(VectorString self, std::vector< std::string >::difference_type i, std::vector< std::string >::value_type const & x)
551  """
552  return _IMP_bff.VectorString___setitem__(self, *args)
553 
554  def pop(self):
555  r"""pop(VectorString self) -> std::vector< std::string >::value_type"""
556  return _IMP_bff.VectorString_pop(self)
557 
558  def append(self, x):
559  r"""append(VectorString self, std::vector< std::string >::value_type const & x)"""
560  return _IMP_bff.VectorString_append(self, x)
561 
562  def empty(self):
563  r"""empty(VectorString self) -> bool"""
564  return _IMP_bff.VectorString_empty(self)
565 
566  def size(self):
567  r"""size(VectorString self) -> std::vector< std::string >::size_type"""
568  return _IMP_bff.VectorString_size(self)
569 
570  def swap(self, v):
571  r"""swap(VectorString self, VectorString v)"""
572  return _IMP_bff.VectorString_swap(self, v)
573 
574  def begin(self):
575  r"""begin(VectorString self) -> std::vector< std::string >::iterator"""
576  return _IMP_bff.VectorString_begin(self)
577 
578  def end(self):
579  r"""end(VectorString self) -> std::vector< std::string >::iterator"""
580  return _IMP_bff.VectorString_end(self)
581 
582  def rbegin(self):
583  r"""rbegin(VectorString self) -> std::vector< std::string >::reverse_iterator"""
584  return _IMP_bff.VectorString_rbegin(self)
585 
586  def rend(self):
587  r"""rend(VectorString self) -> std::vector< std::string >::reverse_iterator"""
588  return _IMP_bff.VectorString_rend(self)
589 
590  def clear(self):
591  r"""clear(VectorString self)"""
592  return _IMP_bff.VectorString_clear(self)
593 
594  def get_allocator(self):
595  r"""get_allocator(VectorString self) -> std::vector< std::string >::allocator_type"""
596  return _IMP_bff.VectorString_get_allocator(self)
597 
598  def pop_back(self):
599  r"""pop_back(VectorString self)"""
600  return _IMP_bff.VectorString_pop_back(self)
601 
602  def erase(self, *args):
603  r"""
604  erase(VectorString self, std::vector< std::string >::iterator pos) -> std::vector< std::string >::iterator
605  erase(VectorString self, std::vector< std::string >::iterator first, std::vector< std::string >::iterator last) -> std::vector< std::string >::iterator
606  """
607  return _IMP_bff.VectorString_erase(self, *args)
608 
609  def __init__(self, *args):
610  r"""
611  __init__(VectorString self) -> VectorString
612  __init__(VectorString self, VectorString other) -> VectorString
613  __init__(VectorString self, std::vector< std::string >::size_type size) -> VectorString
614  __init__(VectorString self, std::vector< std::string >::size_type size, std::vector< std::string >::value_type const & value) -> VectorString
615  """
616  _IMP_bff.VectorString_swiginit(self, _IMP_bff.new_VectorString(*args))
617 
618  def push_back(self, x):
619  r"""push_back(VectorString self, std::vector< std::string >::value_type const & x)"""
620  return _IMP_bff.VectorString_push_back(self, x)
621 
622  def front(self):
623  r"""front(VectorString self) -> std::vector< std::string >::value_type const &"""
624  return _IMP_bff.VectorString_front(self)
625 
626  def back(self):
627  r"""back(VectorString self) -> std::vector< std::string >::value_type const &"""
628  return _IMP_bff.VectorString_back(self)
629 
630  def assign(self, n, x):
631  r"""assign(VectorString self, std::vector< std::string >::size_type n, std::vector< std::string >::value_type const & x)"""
632  return _IMP_bff.VectorString_assign(self, n, x)
633 
634  def resize(self, *args):
635  r"""
636  resize(VectorString self, std::vector< std::string >::size_type new_size)
637  resize(VectorString self, std::vector< std::string >::size_type new_size, std::vector< std::string >::value_type const & x)
638  """
639  return _IMP_bff.VectorString_resize(self, *args)
640 
641  def insert(self, *args):
642  r"""
643  insert(VectorString self, std::vector< std::string >::iterator pos, std::vector< std::string >::value_type const & x) -> std::vector< std::string >::iterator
644  insert(VectorString self, std::vector< std::string >::iterator pos, std::vector< std::string >::size_type n, std::vector< std::string >::value_type const & x)
645  """
646  return _IMP_bff.VectorString_insert(self, *args)
647 
648  def reserve(self, n):
649  r"""reserve(VectorString self, std::vector< std::string >::size_type n)"""
650  return _IMP_bff.VectorString_reserve(self, n)
651 
652  def capacity(self):
653  r"""capacity(VectorString self) -> std::vector< std::string >::size_type"""
654  return _IMP_bff.VectorString_capacity(self)
655  __swig_destroy__ = _IMP_bff.delete_VectorString
656 
657 # Register VectorString in _IMP_bff:
658 _IMP_bff.VectorString_swigregister(VectorString)
659 class VectorDouble(object):
660  r"""Proxy of C++ std::vector< double > class."""
661 
662  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
663  __repr__ = _swig_repr
664 
665  def iterator(self):
666  r"""iterator(VectorDouble self) -> IMP_BFF_SwigPyIterator"""
667  return _IMP_bff.VectorDouble_iterator(self)
668  def __iter__(self):
669  return self.iterator()
670 
671  def __nonzero__(self):
672  r"""__nonzero__(VectorDouble self) -> bool"""
673  return _IMP_bff.VectorDouble___nonzero__(self)
674 
675  def __bool__(self):
676  r"""__bool__(VectorDouble self) -> bool"""
677  return _IMP_bff.VectorDouble___bool__(self)
678 
679  def __len__(self):
680  r"""__len__(VectorDouble self) -> std::vector< double >::size_type"""
681  return _IMP_bff.VectorDouble___len__(self)
682 
683  def __getslice__(self, i, j):
684  r"""__getslice__(VectorDouble self, std::vector< double >::difference_type i, std::vector< double >::difference_type j) -> VectorDouble"""
685  return _IMP_bff.VectorDouble___getslice__(self, i, j)
686 
687  def __setslice__(self, *args):
688  r"""
689  __setslice__(VectorDouble self, std::vector< double >::difference_type i, std::vector< double >::difference_type j)
690  __setslice__(VectorDouble self, std::vector< double >::difference_type i, std::vector< double >::difference_type j, VectorDouble v)
691  """
692  return _IMP_bff.VectorDouble___setslice__(self, *args)
693 
694  def __delslice__(self, i, j):
695  r"""__delslice__(VectorDouble self, std::vector< double >::difference_type i, std::vector< double >::difference_type j)"""
696  return _IMP_bff.VectorDouble___delslice__(self, i, j)
697 
698  def __delitem__(self, *args):
699  r"""
700  __delitem__(VectorDouble self, std::vector< double >::difference_type i)
701  __delitem__(VectorDouble self, SWIGPY_SLICEOBJECT * slice)
702  """
703  return _IMP_bff.VectorDouble___delitem__(self, *args)
704 
705  def __getitem__(self, *args):
706  r"""
707  __getitem__(VectorDouble self, SWIGPY_SLICEOBJECT * slice) -> VectorDouble
708  __getitem__(VectorDouble self, std::vector< double >::difference_type i) -> std::vector< double >::value_type const &
709  """
710  return _IMP_bff.VectorDouble___getitem__(self, *args)
711 
712  def __setitem__(self, *args):
713  r"""
714  __setitem__(VectorDouble self, SWIGPY_SLICEOBJECT * slice, VectorDouble v)
715  __setitem__(VectorDouble self, SWIGPY_SLICEOBJECT * slice)
716  __setitem__(VectorDouble self, std::vector< double >::difference_type i, std::vector< double >::value_type const & x)
717  """
718  return _IMP_bff.VectorDouble___setitem__(self, *args)
719 
720  def pop(self):
721  r"""pop(VectorDouble self) -> std::vector< double >::value_type"""
722  return _IMP_bff.VectorDouble_pop(self)
723 
724  def append(self, x):
725  r"""append(VectorDouble self, std::vector< double >::value_type const & x)"""
726  return _IMP_bff.VectorDouble_append(self, x)
727 
728  def empty(self):
729  r"""empty(VectorDouble self) -> bool"""
730  return _IMP_bff.VectorDouble_empty(self)
731 
732  def size(self):
733  r"""size(VectorDouble self) -> std::vector< double >::size_type"""
734  return _IMP_bff.VectorDouble_size(self)
735 
736  def swap(self, v):
737  r"""swap(VectorDouble self, VectorDouble v)"""
738  return _IMP_bff.VectorDouble_swap(self, v)
739 
740  def begin(self):
741  r"""begin(VectorDouble self) -> std::vector< double >::iterator"""
742  return _IMP_bff.VectorDouble_begin(self)
743 
744  def end(self):
745  r"""end(VectorDouble self) -> std::vector< double >::iterator"""
746  return _IMP_bff.VectorDouble_end(self)
747 
748  def rbegin(self):
749  r"""rbegin(VectorDouble self) -> std::vector< double >::reverse_iterator"""
750  return _IMP_bff.VectorDouble_rbegin(self)
751 
752  def rend(self):
753  r"""rend(VectorDouble self) -> std::vector< double >::reverse_iterator"""
754  return _IMP_bff.VectorDouble_rend(self)
755 
756  def clear(self):
757  r"""clear(VectorDouble self)"""
758  return _IMP_bff.VectorDouble_clear(self)
759 
760  def get_allocator(self):
761  r"""get_allocator(VectorDouble self) -> std::vector< double >::allocator_type"""
762  return _IMP_bff.VectorDouble_get_allocator(self)
763 
764  def pop_back(self):
765  r"""pop_back(VectorDouble self)"""
766  return _IMP_bff.VectorDouble_pop_back(self)
767 
768  def erase(self, *args):
769  r"""
770  erase(VectorDouble self, std::vector< double >::iterator pos) -> std::vector< double >::iterator
771  erase(VectorDouble self, std::vector< double >::iterator first, std::vector< double >::iterator last) -> std::vector< double >::iterator
772  """
773  return _IMP_bff.VectorDouble_erase(self, *args)
774 
775  def __init__(self, *args):
776  r"""
777  __init__(VectorDouble self) -> VectorDouble
778  __init__(VectorDouble self, VectorDouble other) -> VectorDouble
779  __init__(VectorDouble self, std::vector< double >::size_type size) -> VectorDouble
780  __init__(VectorDouble self, std::vector< double >::size_type size, std::vector< double >::value_type const & value) -> VectorDouble
781  """
782  _IMP_bff.VectorDouble_swiginit(self, _IMP_bff.new_VectorDouble(*args))
783 
784  def push_back(self, x):
785  r"""push_back(VectorDouble self, std::vector< double >::value_type const & x)"""
786  return _IMP_bff.VectorDouble_push_back(self, x)
787 
788  def front(self):
789  r"""front(VectorDouble self) -> std::vector< double >::value_type const &"""
790  return _IMP_bff.VectorDouble_front(self)
791 
792  def back(self):
793  r"""back(VectorDouble self) -> std::vector< double >::value_type const &"""
794  return _IMP_bff.VectorDouble_back(self)
795 
796  def assign(self, n, x):
797  r"""assign(VectorDouble self, std::vector< double >::size_type n, std::vector< double >::value_type const & x)"""
798  return _IMP_bff.VectorDouble_assign(self, n, x)
799 
800  def resize(self, *args):
801  r"""
802  resize(VectorDouble self, std::vector< double >::size_type new_size)
803  resize(VectorDouble self, std::vector< double >::size_type new_size, std::vector< double >::value_type const & x)
804  """
805  return _IMP_bff.VectorDouble_resize(self, *args)
806 
807  def insert(self, *args):
808  r"""
809  insert(VectorDouble self, std::vector< double >::iterator pos, std::vector< double >::value_type const & x) -> std::vector< double >::iterator
810  insert(VectorDouble self, std::vector< double >::iterator pos, std::vector< double >::size_type n, std::vector< double >::value_type const & x)
811  """
812  return _IMP_bff.VectorDouble_insert(self, *args)
813 
814  def reserve(self, n):
815  r"""reserve(VectorDouble self, std::vector< double >::size_type n)"""
816  return _IMP_bff.VectorDouble_reserve(self, n)
817 
818  def capacity(self):
819  r"""capacity(VectorDouble self) -> std::vector< double >::size_type"""
820  return _IMP_bff.VectorDouble_capacity(self)
821  __swig_destroy__ = _IMP_bff.delete_VectorDouble
822 
823 # Register VectorDouble in _IMP_bff:
824 _IMP_bff.VectorDouble_swigregister(VectorDouble)
825 class VectorFloat(object):
826  r"""Proxy of C++ std::vector< float > class."""
827 
828  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
829  __repr__ = _swig_repr
830 
831  def iterator(self):
832  r"""iterator(VectorFloat self) -> IMP_BFF_SwigPyIterator"""
833  return _IMP_bff.VectorFloat_iterator(self)
834  def __iter__(self):
835  return self.iterator()
836 
837  def __nonzero__(self):
838  r"""__nonzero__(VectorFloat self) -> bool"""
839  return _IMP_bff.VectorFloat___nonzero__(self)
840 
841  def __bool__(self):
842  r"""__bool__(VectorFloat self) -> bool"""
843  return _IMP_bff.VectorFloat___bool__(self)
844 
845  def __len__(self):
846  r"""__len__(VectorFloat self) -> std::vector< float >::size_type"""
847  return _IMP_bff.VectorFloat___len__(self)
848 
849  def __getslice__(self, i, j):
850  r"""__getslice__(VectorFloat self, std::vector< float >::difference_type i, std::vector< float >::difference_type j) -> VectorFloat"""
851  return _IMP_bff.VectorFloat___getslice__(self, i, j)
852 
853  def __setslice__(self, *args):
854  r"""
855  __setslice__(VectorFloat self, std::vector< float >::difference_type i, std::vector< float >::difference_type j)
856  __setslice__(VectorFloat self, std::vector< float >::difference_type i, std::vector< float >::difference_type j, VectorFloat v)
857  """
858  return _IMP_bff.VectorFloat___setslice__(self, *args)
859 
860  def __delslice__(self, i, j):
861  r"""__delslice__(VectorFloat self, std::vector< float >::difference_type i, std::vector< float >::difference_type j)"""
862  return _IMP_bff.VectorFloat___delslice__(self, i, j)
863 
864  def __delitem__(self, *args):
865  r"""
866  __delitem__(VectorFloat self, std::vector< float >::difference_type i)
867  __delitem__(VectorFloat self, SWIGPY_SLICEOBJECT * slice)
868  """
869  return _IMP_bff.VectorFloat___delitem__(self, *args)
870 
871  def __getitem__(self, *args):
872  r"""
873  __getitem__(VectorFloat self, SWIGPY_SLICEOBJECT * slice) -> VectorFloat
874  __getitem__(VectorFloat self, std::vector< float >::difference_type i) -> std::vector< float >::value_type const &
875  """
876  return _IMP_bff.VectorFloat___getitem__(self, *args)
877 
878  def __setitem__(self, *args):
879  r"""
880  __setitem__(VectorFloat self, SWIGPY_SLICEOBJECT * slice, VectorFloat v)
881  __setitem__(VectorFloat self, SWIGPY_SLICEOBJECT * slice)
882  __setitem__(VectorFloat self, std::vector< float >::difference_type i, std::vector< float >::value_type const & x)
883  """
884  return _IMP_bff.VectorFloat___setitem__(self, *args)
885 
886  def pop(self):
887  r"""pop(VectorFloat self) -> std::vector< float >::value_type"""
888  return _IMP_bff.VectorFloat_pop(self)
889 
890  def append(self, x):
891  r"""append(VectorFloat self, std::vector< float >::value_type const & x)"""
892  return _IMP_bff.VectorFloat_append(self, x)
893 
894  def empty(self):
895  r"""empty(VectorFloat self) -> bool"""
896  return _IMP_bff.VectorFloat_empty(self)
897 
898  def size(self):
899  r"""size(VectorFloat self) -> std::vector< float >::size_type"""
900  return _IMP_bff.VectorFloat_size(self)
901 
902  def swap(self, v):
903  r"""swap(VectorFloat self, VectorFloat v)"""
904  return _IMP_bff.VectorFloat_swap(self, v)
905 
906  def begin(self):
907  r"""begin(VectorFloat self) -> std::vector< float >::iterator"""
908  return _IMP_bff.VectorFloat_begin(self)
909 
910  def end(self):
911  r"""end(VectorFloat self) -> std::vector< float >::iterator"""
912  return _IMP_bff.VectorFloat_end(self)
913 
914  def rbegin(self):
915  r"""rbegin(VectorFloat self) -> std::vector< float >::reverse_iterator"""
916  return _IMP_bff.VectorFloat_rbegin(self)
917 
918  def rend(self):
919  r"""rend(VectorFloat self) -> std::vector< float >::reverse_iterator"""
920  return _IMP_bff.VectorFloat_rend(self)
921 
922  def clear(self):
923  r"""clear(VectorFloat self)"""
924  return _IMP_bff.VectorFloat_clear(self)
925 
926  def get_allocator(self):
927  r"""get_allocator(VectorFloat self) -> std::vector< float >::allocator_type"""
928  return _IMP_bff.VectorFloat_get_allocator(self)
929 
930  def pop_back(self):
931  r"""pop_back(VectorFloat self)"""
932  return _IMP_bff.VectorFloat_pop_back(self)
933 
934  def erase(self, *args):
935  r"""
936  erase(VectorFloat self, std::vector< float >::iterator pos) -> std::vector< float >::iterator
937  erase(VectorFloat self, std::vector< float >::iterator first, std::vector< float >::iterator last) -> std::vector< float >::iterator
938  """
939  return _IMP_bff.VectorFloat_erase(self, *args)
940 
941  def __init__(self, *args):
942  r"""
943  __init__(VectorFloat self) -> VectorFloat
944  __init__(VectorFloat self, VectorFloat other) -> VectorFloat
945  __init__(VectorFloat self, std::vector< float >::size_type size) -> VectorFloat
946  __init__(VectorFloat self, std::vector< float >::size_type size, std::vector< float >::value_type const & value) -> VectorFloat
947  """
948  _IMP_bff.VectorFloat_swiginit(self, _IMP_bff.new_VectorFloat(*args))
949 
950  def push_back(self, x):
951  r"""push_back(VectorFloat self, std::vector< float >::value_type const & x)"""
952  return _IMP_bff.VectorFloat_push_back(self, x)
953 
954  def front(self):
955  r"""front(VectorFloat self) -> std::vector< float >::value_type const &"""
956  return _IMP_bff.VectorFloat_front(self)
957 
958  def back(self):
959  r"""back(VectorFloat self) -> std::vector< float >::value_type const &"""
960  return _IMP_bff.VectorFloat_back(self)
961 
962  def assign(self, n, x):
963  r"""assign(VectorFloat self, std::vector< float >::size_type n, std::vector< float >::value_type const & x)"""
964  return _IMP_bff.VectorFloat_assign(self, n, x)
965 
966  def resize(self, *args):
967  r"""
968  resize(VectorFloat self, std::vector< float >::size_type new_size)
969  resize(VectorFloat self, std::vector< float >::size_type new_size, std::vector< float >::value_type const & x)
970  """
971  return _IMP_bff.VectorFloat_resize(self, *args)
972 
973  def insert(self, *args):
974  r"""
975  insert(VectorFloat self, std::vector< float >::iterator pos, std::vector< float >::value_type const & x) -> std::vector< float >::iterator
976  insert(VectorFloat self, std::vector< float >::iterator pos, std::vector< float >::size_type n, std::vector< float >::value_type const & x)
977  """
978  return _IMP_bff.VectorFloat_insert(self, *args)
979 
980  def reserve(self, n):
981  r"""reserve(VectorFloat self, std::vector< float >::size_type n)"""
982  return _IMP_bff.VectorFloat_reserve(self, n)
983 
984  def capacity(self):
985  r"""capacity(VectorFloat self) -> std::vector< float >::size_type"""
986  return _IMP_bff.VectorFloat_capacity(self)
987  __swig_destroy__ = _IMP_bff.delete_VectorFloat
988 
989 # Register VectorFloat in _IMP_bff:
990 _IMP_bff.VectorFloat_swigregister(VectorFloat)
991 class VectorInt(object):
992  r"""Proxy of C++ std::vector< int > class."""
993 
994  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
995  __repr__ = _swig_repr
996 
997  def iterator(self):
998  r"""iterator(VectorInt self) -> IMP_BFF_SwigPyIterator"""
999  return _IMP_bff.VectorInt_iterator(self)
1000  def __iter__(self):
1001  return self.iterator()
1002 
1003  def __nonzero__(self):
1004  r"""__nonzero__(VectorInt self) -> bool"""
1005  return _IMP_bff.VectorInt___nonzero__(self)
1006 
1007  def __bool__(self):
1008  r"""__bool__(VectorInt self) -> bool"""
1009  return _IMP_bff.VectorInt___bool__(self)
1010 
1011  def __len__(self):
1012  r"""__len__(VectorInt self) -> std::vector< int >::size_type"""
1013  return _IMP_bff.VectorInt___len__(self)
1014 
1015  def __getslice__(self, i, j):
1016  r"""__getslice__(VectorInt self, std::vector< int >::difference_type i, std::vector< int >::difference_type j) -> VectorInt"""
1017  return _IMP_bff.VectorInt___getslice__(self, i, j)
1018 
1019  def __setslice__(self, *args):
1020  r"""
1021  __setslice__(VectorInt self, std::vector< int >::difference_type i, std::vector< int >::difference_type j)
1022  __setslice__(VectorInt self, std::vector< int >::difference_type i, std::vector< int >::difference_type j, VectorInt v)
1023  """
1024  return _IMP_bff.VectorInt___setslice__(self, *args)
1025 
1026  def __delslice__(self, i, j):
1027  r"""__delslice__(VectorInt self, std::vector< int >::difference_type i, std::vector< int >::difference_type j)"""
1028  return _IMP_bff.VectorInt___delslice__(self, i, j)
1029 
1030  def __delitem__(self, *args):
1031  r"""
1032  __delitem__(VectorInt self, std::vector< int >::difference_type i)
1033  __delitem__(VectorInt self, SWIGPY_SLICEOBJECT * slice)
1034  """
1035  return _IMP_bff.VectorInt___delitem__(self, *args)
1036 
1037  def __getitem__(self, *args):
1038  r"""
1039  __getitem__(VectorInt self, SWIGPY_SLICEOBJECT * slice) -> VectorInt
1040  __getitem__(VectorInt self, std::vector< int >::difference_type i) -> std::vector< int >::value_type const &
1041  """
1042  return _IMP_bff.VectorInt___getitem__(self, *args)
1043 
1044  def __setitem__(self, *args):
1045  r"""
1046  __setitem__(VectorInt self, SWIGPY_SLICEOBJECT * slice, VectorInt v)
1047  __setitem__(VectorInt self, SWIGPY_SLICEOBJECT * slice)
1048  __setitem__(VectorInt self, std::vector< int >::difference_type i, std::vector< int >::value_type const & x)
1049  """
1050  return _IMP_bff.VectorInt___setitem__(self, *args)
1051 
1052  def pop(self):
1053  r"""pop(VectorInt self) -> std::vector< int >::value_type"""
1054  return _IMP_bff.VectorInt_pop(self)
1055 
1056  def append(self, x):
1057  r"""append(VectorInt self, std::vector< int >::value_type const & x)"""
1058  return _IMP_bff.VectorInt_append(self, x)
1059 
1060  def empty(self):
1061  r"""empty(VectorInt self) -> bool"""
1062  return _IMP_bff.VectorInt_empty(self)
1063 
1064  def size(self):
1065  r"""size(VectorInt self) -> std::vector< int >::size_type"""
1066  return _IMP_bff.VectorInt_size(self)
1067 
1068  def swap(self, v):
1069  r"""swap(VectorInt self, VectorInt v)"""
1070  return _IMP_bff.VectorInt_swap(self, v)
1071 
1072  def begin(self):
1073  r"""begin(VectorInt self) -> std::vector< int >::iterator"""
1074  return _IMP_bff.VectorInt_begin(self)
1075 
1076  def end(self):
1077  r"""end(VectorInt self) -> std::vector< int >::iterator"""
1078  return _IMP_bff.VectorInt_end(self)
1079 
1080  def rbegin(self):
1081  r"""rbegin(VectorInt self) -> std::vector< int >::reverse_iterator"""
1082  return _IMP_bff.VectorInt_rbegin(self)
1083 
1084  def rend(self):
1085  r"""rend(VectorInt self) -> std::vector< int >::reverse_iterator"""
1086  return _IMP_bff.VectorInt_rend(self)
1087 
1088  def clear(self):
1089  r"""clear(VectorInt self)"""
1090  return _IMP_bff.VectorInt_clear(self)
1091 
1092  def get_allocator(self):
1093  r"""get_allocator(VectorInt self) -> std::vector< int >::allocator_type"""
1094  return _IMP_bff.VectorInt_get_allocator(self)
1095 
1096  def pop_back(self):
1097  r"""pop_back(VectorInt self)"""
1098  return _IMP_bff.VectorInt_pop_back(self)
1099 
1100  def erase(self, *args):
1101  r"""
1102  erase(VectorInt self, std::vector< int >::iterator pos) -> std::vector< int >::iterator
1103  erase(VectorInt self, std::vector< int >::iterator first, std::vector< int >::iterator last) -> std::vector< int >::iterator
1104  """
1105  return _IMP_bff.VectorInt_erase(self, *args)
1106 
1107  def __init__(self, *args):
1108  r"""
1109  __init__(VectorInt self) -> VectorInt
1110  __init__(VectorInt self, VectorInt other) -> VectorInt
1111  __init__(VectorInt self, std::vector< int >::size_type size) -> VectorInt
1112  __init__(VectorInt self, std::vector< int >::size_type size, std::vector< int >::value_type const & value) -> VectorInt
1113  """
1114  _IMP_bff.VectorInt_swiginit(self, _IMP_bff.new_VectorInt(*args))
1115 
1116  def push_back(self, x):
1117  r"""push_back(VectorInt self, std::vector< int >::value_type const & x)"""
1118  return _IMP_bff.VectorInt_push_back(self, x)
1119 
1120  def front(self):
1121  r"""front(VectorInt self) -> std::vector< int >::value_type const &"""
1122  return _IMP_bff.VectorInt_front(self)
1123 
1124  def back(self):
1125  r"""back(VectorInt self) -> std::vector< int >::value_type const &"""
1126  return _IMP_bff.VectorInt_back(self)
1127 
1128  def assign(self, n, x):
1129  r"""assign(VectorInt self, std::vector< int >::size_type n, std::vector< int >::value_type const & x)"""
1130  return _IMP_bff.VectorInt_assign(self, n, x)
1131 
1132  def resize(self, *args):
1133  r"""
1134  resize(VectorInt self, std::vector< int >::size_type new_size)
1135  resize(VectorInt self, std::vector< int >::size_type new_size, std::vector< int >::value_type const & x)
1136  """
1137  return _IMP_bff.VectorInt_resize(self, *args)
1138 
1139  def insert(self, *args):
1140  r"""
1141  insert(VectorInt self, std::vector< int >::iterator pos, std::vector< int >::value_type const & x) -> std::vector< int >::iterator
1142  insert(VectorInt self, std::vector< int >::iterator pos, std::vector< int >::size_type n, std::vector< int >::value_type const & x)
1143  """
1144  return _IMP_bff.VectorInt_insert(self, *args)
1145 
1146  def reserve(self, n):
1147  r"""reserve(VectorInt self, std::vector< int >::size_type n)"""
1148  return _IMP_bff.VectorInt_reserve(self, n)
1149 
1150  def capacity(self):
1151  r"""capacity(VectorInt self) -> std::vector< int >::size_type"""
1152  return _IMP_bff.VectorInt_capacity(self)
1153  __swig_destroy__ = _IMP_bff.delete_VectorInt
1154 
1155 # Register VectorInt in _IMP_bff:
1156 _IMP_bff.VectorInt_swigregister(VectorInt)
1157 class VectorLong(object):
1158  r"""Proxy of C++ std::vector< long > class."""
1159 
1160  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1161  __repr__ = _swig_repr
1162 
1163  def iterator(self):
1164  r"""iterator(VectorLong self) -> IMP_BFF_SwigPyIterator"""
1165  return _IMP_bff.VectorLong_iterator(self)
1166  def __iter__(self):
1167  return self.iterator()
1168 
1169  def __nonzero__(self):
1170  r"""__nonzero__(VectorLong self) -> bool"""
1171  return _IMP_bff.VectorLong___nonzero__(self)
1172 
1173  def __bool__(self):
1174  r"""__bool__(VectorLong self) -> bool"""
1175  return _IMP_bff.VectorLong___bool__(self)
1176 
1177  def __len__(self):
1178  r"""__len__(VectorLong self) -> std::vector< long >::size_type"""
1179  return _IMP_bff.VectorLong___len__(self)
1180 
1181  def __getslice__(self, i, j):
1182  r"""__getslice__(VectorLong self, std::vector< long >::difference_type i, std::vector< long >::difference_type j) -> VectorLong"""
1183  return _IMP_bff.VectorLong___getslice__(self, i, j)
1184 
1185  def __setslice__(self, *args):
1186  r"""
1187  __setslice__(VectorLong self, std::vector< long >::difference_type i, std::vector< long >::difference_type j)
1188  __setslice__(VectorLong self, std::vector< long >::difference_type i, std::vector< long >::difference_type j, VectorLong v)
1189  """
1190  return _IMP_bff.VectorLong___setslice__(self, *args)
1191 
1192  def __delslice__(self, i, j):
1193  r"""__delslice__(VectorLong self, std::vector< long >::difference_type i, std::vector< long >::difference_type j)"""
1194  return _IMP_bff.VectorLong___delslice__(self, i, j)
1195 
1196  def __delitem__(self, *args):
1197  r"""
1198  __delitem__(VectorLong self, std::vector< long >::difference_type i)
1199  __delitem__(VectorLong self, SWIGPY_SLICEOBJECT * slice)
1200  """
1201  return _IMP_bff.VectorLong___delitem__(self, *args)
1202 
1203  def __getitem__(self, *args):
1204  r"""
1205  __getitem__(VectorLong self, SWIGPY_SLICEOBJECT * slice) -> VectorLong
1206  __getitem__(VectorLong self, std::vector< long >::difference_type i) -> std::vector< long >::value_type const &
1207  """
1208  return _IMP_bff.VectorLong___getitem__(self, *args)
1209 
1210  def __setitem__(self, *args):
1211  r"""
1212  __setitem__(VectorLong self, SWIGPY_SLICEOBJECT * slice, VectorLong v)
1213  __setitem__(VectorLong self, SWIGPY_SLICEOBJECT * slice)
1214  __setitem__(VectorLong self, std::vector< long >::difference_type i, std::vector< long >::value_type const & x)
1215  """
1216  return _IMP_bff.VectorLong___setitem__(self, *args)
1217 
1218  def pop(self):
1219  r"""pop(VectorLong self) -> std::vector< long >::value_type"""
1220  return _IMP_bff.VectorLong_pop(self)
1221 
1222  def append(self, x):
1223  r"""append(VectorLong self, std::vector< long >::value_type const & x)"""
1224  return _IMP_bff.VectorLong_append(self, x)
1225 
1226  def empty(self):
1227  r"""empty(VectorLong self) -> bool"""
1228  return _IMP_bff.VectorLong_empty(self)
1229 
1230  def size(self):
1231  r"""size(VectorLong self) -> std::vector< long >::size_type"""
1232  return _IMP_bff.VectorLong_size(self)
1233 
1234  def swap(self, v):
1235  r"""swap(VectorLong self, VectorLong v)"""
1236  return _IMP_bff.VectorLong_swap(self, v)
1237 
1238  def begin(self):
1239  r"""begin(VectorLong self) -> std::vector< long >::iterator"""
1240  return _IMP_bff.VectorLong_begin(self)
1241 
1242  def end(self):
1243  r"""end(VectorLong self) -> std::vector< long >::iterator"""
1244  return _IMP_bff.VectorLong_end(self)
1245 
1246  def rbegin(self):
1247  r"""rbegin(VectorLong self) -> std::vector< long >::reverse_iterator"""
1248  return _IMP_bff.VectorLong_rbegin(self)
1249 
1250  def rend(self):
1251  r"""rend(VectorLong self) -> std::vector< long >::reverse_iterator"""
1252  return _IMP_bff.VectorLong_rend(self)
1253 
1254  def clear(self):
1255  r"""clear(VectorLong self)"""
1256  return _IMP_bff.VectorLong_clear(self)
1257 
1258  def get_allocator(self):
1259  r"""get_allocator(VectorLong self) -> std::vector< long >::allocator_type"""
1260  return _IMP_bff.VectorLong_get_allocator(self)
1261 
1262  def pop_back(self):
1263  r"""pop_back(VectorLong self)"""
1264  return _IMP_bff.VectorLong_pop_back(self)
1265 
1266  def erase(self, *args):
1267  r"""
1268  erase(VectorLong self, std::vector< long >::iterator pos) -> std::vector< long >::iterator
1269  erase(VectorLong self, std::vector< long >::iterator first, std::vector< long >::iterator last) -> std::vector< long >::iterator
1270  """
1271  return _IMP_bff.VectorLong_erase(self, *args)
1272 
1273  def __init__(self, *args):
1274  r"""
1275  __init__(VectorLong self) -> VectorLong
1276  __init__(VectorLong self, VectorLong other) -> VectorLong
1277  __init__(VectorLong self, std::vector< long >::size_type size) -> VectorLong
1278  __init__(VectorLong self, std::vector< long >::size_type size, std::vector< long >::value_type const & value) -> VectorLong
1279  """
1280  _IMP_bff.VectorLong_swiginit(self, _IMP_bff.new_VectorLong(*args))
1281 
1282  def push_back(self, x):
1283  r"""push_back(VectorLong self, std::vector< long >::value_type const & x)"""
1284  return _IMP_bff.VectorLong_push_back(self, x)
1285 
1286  def front(self):
1287  r"""front(VectorLong self) -> std::vector< long >::value_type const &"""
1288  return _IMP_bff.VectorLong_front(self)
1289 
1290  def back(self):
1291  r"""back(VectorLong self) -> std::vector< long >::value_type const &"""
1292  return _IMP_bff.VectorLong_back(self)
1293 
1294  def assign(self, n, x):
1295  r"""assign(VectorLong self, std::vector< long >::size_type n, std::vector< long >::value_type const & x)"""
1296  return _IMP_bff.VectorLong_assign(self, n, x)
1297 
1298  def resize(self, *args):
1299  r"""
1300  resize(VectorLong self, std::vector< long >::size_type new_size)
1301  resize(VectorLong self, std::vector< long >::size_type new_size, std::vector< long >::value_type const & x)
1302  """
1303  return _IMP_bff.VectorLong_resize(self, *args)
1304 
1305  def insert(self, *args):
1306  r"""
1307  insert(VectorLong self, std::vector< long >::iterator pos, std::vector< long >::value_type const & x) -> std::vector< long >::iterator
1308  insert(VectorLong self, std::vector< long >::iterator pos, std::vector< long >::size_type n, std::vector< long >::value_type const & x)
1309  """
1310  return _IMP_bff.VectorLong_insert(self, *args)
1311 
1312  def reserve(self, n):
1313  r"""reserve(VectorLong self, std::vector< long >::size_type n)"""
1314  return _IMP_bff.VectorLong_reserve(self, n)
1315 
1316  def capacity(self):
1317  r"""capacity(VectorLong self) -> std::vector< long >::size_type"""
1318  return _IMP_bff.VectorLong_capacity(self)
1319  __swig_destroy__ = _IMP_bff.delete_VectorLong
1320 
1321 # Register VectorLong in _IMP_bff:
1322 _IMP_bff.VectorLong_swigregister(VectorLong)
1323 
1324 PathMapTileEdges=list
1325 _plural_types.append("PathMapTileEdges")
1326 _value_types.append("PathMapTileEdge")
1327 
1328 
1329 _object_types.append("PathMap")
1330 
1331 
1332 def _object_cast_to_PathMap(o):
1333  r"""_object_cast_to_PathMap(Object o) -> PathMap"""
1334  return _IMP_bff._object_cast_to_PathMap(o)
1335 class PathMapHeader(object):
1336  r"""Proxy of C++ IMP::bff::PathMapHeader class."""
1337 
1338  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1339  __repr__ = _swig_repr
1340  __swig_destroy__ = _IMP_bff.delete_PathMapHeader
1341 
1342  def __init__(self, *args, **kwargs):
1343  r"""__init__(PathMapHeader self, double max_path_length=10.0, double grid_spacing=1.0, double neighbor_radius=2, double obstacle_threshold=std::numeric_limits< double >::epsilon()) -> PathMapHeader"""
1344  _IMP_bff.PathMapHeader_swiginit(self, _IMP_bff.new_PathMapHeader(*args, **kwargs))
1345 
1346  def update_map_dimensions(self, nx=-1, ny=-1, nz=-1):
1347  r"""update_map_dimensions(PathMapHeader self, int nx=-1, int ny=-1, int nz=-1)"""
1348  return _IMP_bff.PathMapHeader_update_map_dimensions(self, nx, ny, nz)
1349 
1350  def set_path_origin(self, v):
1351  r"""set_path_origin(PathMapHeader self, Vector3D v)"""
1352  return _IMP_bff.PathMapHeader_set_path_origin(self, v)
1353 
1354  def get_path_origin(self):
1355  r"""get_path_origin(PathMapHeader self) -> Vector3D"""
1356  return _IMP_bff.PathMapHeader_get_path_origin(self)
1357 
1358  def get_max_path_length(self):
1359  r"""get_max_path_length(PathMapHeader self) -> double"""
1360  return _IMP_bff.PathMapHeader_get_max_path_length(self)
1361 
1362  def get_simulation_grid_resolution(self):
1363  r"""get_simulation_grid_resolution(PathMapHeader self) -> double"""
1364  return _IMP_bff.PathMapHeader_get_simulation_grid_resolution(self)
1365 
1366  def set_obstacle_threshold(self, obstacle_threshold):
1367  r"""set_obstacle_threshold(PathMapHeader self, double obstacle_threshold)"""
1368  return _IMP_bff.PathMapHeader_set_obstacle_threshold(self, obstacle_threshold)
1369 
1370  def get_obstacle_threshold(self):
1371  r"""get_obstacle_threshold(PathMapHeader self) -> double"""
1372  return _IMP_bff.PathMapHeader_get_obstacle_threshold(self)
1373 
1374  def set_neighbor_radius(self, neighbor_radius):
1375  r"""set_neighbor_radius(PathMapHeader self, double neighbor_radius)"""
1376  return _IMP_bff.PathMapHeader_set_neighbor_radius(self, neighbor_radius)
1377 
1378  def get_neighbor_radius(self):
1379  r"""get_neighbor_radius(PathMapHeader self) -> double"""
1380  return _IMP_bff.PathMapHeader_get_neighbor_radius(self)
1381 
1382  def get_neighbor_box_size(self):
1383  r"""get_neighbor_box_size(PathMapHeader self) -> int"""
1384  return _IMP_bff.PathMapHeader_get_neighbor_box_size(self)
1385 
1386  def get_density_header(self):
1387  r"""get_density_header(PathMapHeader self) -> DensityHeader"""
1388  return _IMP_bff.PathMapHeader_get_density_header(self)
1389 
1390  def get_density_header_writable(self):
1391  r"""get_density_header_writable(PathMapHeader self) -> DensityHeader"""
1392  return _IMP_bff.PathMapHeader_get_density_header_writable(self)
1393 
1394  def get_origin(self):
1395  r"""get_origin(PathMapHeader self) -> Vector3D"""
1396  return _IMP_bff.PathMapHeader_get_origin(self)
1397 
1398  def get_grid_edge_length(self):
1399  r"""get_grid_edge_length(PathMapHeader self) -> double"""
1400  return _IMP_bff.PathMapHeader_get_grid_edge_length(self)
1401 
1402  def set_origin(self, x, y, z):
1403  r"""set_origin(PathMapHeader self, float x, float y, float z)"""
1404  return _IMP_bff.PathMapHeader_set_origin(self, x, y, z)
1405 
1406  def show(self, *args, **kwargs):
1407  r"""show(PathMapHeader self, _ostream out=std::cout)"""
1408  return _IMP_bff.PathMapHeader_show(self, *args, **kwargs)
1409 
1410 # Register PathMapHeader in _IMP_bff:
1411 _IMP_bff.PathMapHeader_swigregister(PathMapHeader)
1412 class PathMap(IMP.em.SampledDensityMap):
1413  r"""Proxy of C++ IMP::bff::PathMap class."""
1414 
1415  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1416 
1417  def update_tiles(self, *args, **kwargs):
1418  r"""update_tiles(PathMap self, float obstacle_threshold=-1.0, bool binarize=True, float obstacle_penalty=TILE_PENALTY_DEFAULT, bool reset_tile_edges=True)"""
1419  return _IMP_bff.PathMap_update_tiles(self, *args, **kwargs)
1420 
1421  def resize(self, nvox):
1422  r"""resize(PathMap self, unsigned int nvox)"""
1423  return _IMP_bff.PathMap_resize(self, nvox)
1424 
1425  def set_data(self, *args, **kwargs):
1426  r"""set_data(PathMap self, double * input, float obstacle_threshold=-1, bool binarize=True, float obstacle_penalty=TILE_PENALTY_DEFAULT)"""
1427  return _IMP_bff.PathMap_set_data(self, *args, **kwargs)
1428 
1429  def get_neighbor_idx_offsets(self, neighbor_radius=-1):
1430  r"""get_neighbor_idx_offsets(PathMap self, double neighbor_radius=-1) -> VectorInt"""
1431  return _IMP_bff.PathMap_get_neighbor_idx_offsets(self, neighbor_radius)
1432 
1433  def get_dim_index_by_voxel(self, index, dim):
1434  r"""get_dim_index_by_voxel(PathMap self, long index, int dim) -> int"""
1435  return _IMP_bff.PathMap_get_dim_index_by_voxel(self, index, dim)
1436 
1437  def get_path_map_header(self):
1438  h = _IMP_bff.DensityMap_get_path_map_header(self)
1439  h._owner = self
1440  return h
1441 
1442 
1443 
1444  def get_path_map_header_writable(self):
1445  h = _IMP_bff.PathMap_get_path_map_header_writable(self)
1446  h._owner = self
1447  return h
1448 
1449 
1450 
1451  def set_path_map_header(self, path_map_header, resolution=-1.0):
1452  r"""set_path_map_header(PathMap self, PathMapHeader path_map_header, float resolution=-1.0)"""
1453  return _IMP_bff.PathMap_set_path_map_header(self, path_map_header, resolution)
1454 
1455  def get_tile_values(self, *args, **kwargs):
1456  r"""
1457  get_tile_values(PathMap self, int value_type=PM_TILE_COST, PairFloatFloat bounds=std::pair< float,float >(
1458  {std::numeric_limits<float>::min(),
1459  std::numeric_limits<float>::max()}), std::string const & feature_name="")
1460  """
1461  return _IMP_bff.PathMap_get_tile_values(self, *args, **kwargs)
1462 
1463  def get_tiles(self):
1464  r"""get_tiles(PathMap self) -> VectorPathMapTile"""
1465  return _IMP_bff.PathMap_get_tiles(self)
1466 
1467  def fill_sphere(self, r0, radius, value, inverse=True):
1468  r"""fill_sphere(PathMap self, Vector3D r0, double radius, double value, bool inverse=True)"""
1469  return _IMP_bff.PathMap_fill_sphere(self, r0, radius, value, inverse)
1470 
1471  def find_path(self, path_begin_idx, path_end_idx=-1, heuristic_mode=0):
1472  r"""find_path(PathMap self, long path_begin_idx, long path_end_idx=-1, int heuristic_mode=0)"""
1473  return _IMP_bff.PathMap_find_path(self, path_begin_idx, path_end_idx, heuristic_mode)
1474 
1475  def find_path_dijkstra(self, path_begin_idx, path_end_idx=-1):
1476  r"""find_path_dijkstra(PathMap self, long path_begin_idx, long path_end_idx=-1)"""
1477  return _IMP_bff.PathMap_find_path_dijkstra(self, path_begin_idx, path_end_idx)
1478 
1479  def find_path_astar(self, path_begin_idx, path_end_idx=-1):
1480  r"""find_path_astar(PathMap self, long path_begin_idx, long path_end_idx=-1)"""
1481  return _IMP_bff.PathMap_find_path_astar(self, path_begin_idx, path_end_idx)
1482 
1483  def get_xyz_density(self):
1484  r"""get_xyz_density(PathMap self)"""
1485  return _IMP_bff.PathMap_get_xyz_density(self)
1486 
1487  def sample_obstacles(self, extra_radius=0.0):
1488  r"""sample_obstacles(PathMap self, double extra_radius=0.0)"""
1489  return _IMP_bff.PathMap_sample_obstacles(self, extra_radius)
1490 
1491  def __init__(self, *args, **kwargs):
1492  r"""__init__(PathMap self, PathMapHeader header, std::string name="PathMap%1%", IMP::em::KernelType kt=BINARIZED_SPHERE, float resolution=-1.0) -> PathMap"""
1493  _IMP_bff.PathMap_swiginit(self, _IMP_bff.new_PathMap(*args, **kwargs))
1494 
1495  def __str__(self):
1496  r"""__str__(PathMap self) -> std::string"""
1497  return _IMP_bff.PathMap___str__(self)
1498 
1499  def __repr__(self):
1500  r"""__repr__(PathMap self) -> std::string"""
1501  return _IMP_bff.PathMap___repr__(self)
1502 
1503  @staticmethod
1504  def get_from(o):
1505  return _object_cast_to_PathMap(o)
1506 
1507  __swig_destroy__ = _IMP_bff.delete_PathMap
1508 
1509 # Register PathMap in _IMP_bff:
1510 _IMP_bff.PathMap_swigregister(PathMap)
1511 
1512 def write_path_map(*args, **kwargs):
1513  r"""
1514  write_path_map(PathMap m, std::string filename, int value_type, PairFloatFloat bounds=std::pair< float,float >(
1515  std::numeric_limits<float>::min(),
1516  std::numeric_limits<float>::max()
1517  ), std::string const & feature_name="")
1518  """
1519  return _IMP_bff.write_path_map(*args, **kwargs)
1520 PM_TILE_PENALTY = _IMP_bff.PM_TILE_PENALTY
1521 
1522 PM_TILE_COST = _IMP_bff.PM_TILE_COST
1523 
1524 PM_TILE_DENSITY = _IMP_bff.PM_TILE_DENSITY
1525 
1526 PM_TILE_COST_DENSITY = _IMP_bff.PM_TILE_COST_DENSITY
1527 
1528 PM_TILE_PATH_LENGTH = _IMP_bff.PM_TILE_PATH_LENGTH
1529 
1530 PM_TILE_PATH_LENGTH_DENSITY = _IMP_bff.PM_TILE_PATH_LENGTH_DENSITY
1531 
1532 PM_TILE_FEATURE = _IMP_bff.PM_TILE_FEATURE
1533 
1534 PM_TILE_ACCESSIBLE_DENSITY = _IMP_bff.PM_TILE_ACCESSIBLE_DENSITY
1535 
1536 PM_TILE_ACCESSIBLE_FEATURE = _IMP_bff.PM_TILE_ACCESSIBLE_FEATURE
1537 
1538 class PathMapTile(object):
1539  r"""Proxy of C++ IMP::bff::PathMapTile class."""
1540 
1541  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1542  __repr__ = _swig_repr
1543  density = property(_IMP_bff.PathMapTile_density_get, _IMP_bff.PathMapTile_density_set, doc=r"""density : float""")
1544 
1545  def __init__(self, index=-1, visit_penalty=0.0, tile_density=1.0):
1546  r"""__init__(PathMapTile self, long index=-1, float visit_penalty=0.0, float tile_density=1.0) -> PathMapTile"""
1547  _IMP_bff.PathMapTile_swiginit(self, _IMP_bff.new_PathMapTile(index, visit_penalty, tile_density))
1548 
1549  def backtrack_to_path(self):
1550  r"""backtrack_to_path(PathMapTile self) -> VectorLong"""
1551  return _IMP_bff.PathMapTile_backtrack_to_path(self)
1552 
1553  def get_value(self, *args, **kwargs):
1554  r"""
1555  get_value(PathMapTile self, int value_type, PairFloatFloat bounds=std::pair< float,float >(
1556  {std::numeric_limits<float>::min(),
1557  std::numeric_limits<float>::max()}), std::string const & feature_name="", float grid_spacing=1.0) -> float
1558  """
1559  return _IMP_bff.PathMapTile_get_value(self, *args, **kwargs)
1560 
1561  def set_value(self, *args, **kwargs):
1562  r"""set_value(PathMapTile self, int value_type, float value, std::string const & name="")"""
1563  return _IMP_bff.PathMapTile_set_value(self, *args, **kwargs)
1564  __swig_destroy__ = _IMP_bff.delete_PathMapTile
1565 
1566 # Register PathMapTile in _IMP_bff:
1567 _IMP_bff.PathMapTile_swigregister(PathMapTile)
1568 cvar = _IMP_bff.cvar
1569 TILE_VISITED_DEFAULT = cvar.TILE_VISITED_DEFAULT
1570 TILE_PENALTY_DEFAULT = cvar.TILE_PENALTY_DEFAULT
1571 TILE_COST_DEFAULT = cvar.TILE_COST_DEFAULT
1572 TILE_EDGE_COST_DEFAULT = cvar.TILE_EDGE_COST_DEFAULT
1573 TILE_PENALTY_THRESHOLD = cvar.TILE_PENALTY_THRESHOLD
1574 TILE_OBSTACLE_THRESHOLD = cvar.TILE_OBSTACLE_THRESHOLD
1575 TILE_OBSTACLE_PENALTY = cvar.TILE_OBSTACLE_PENALTY
1576 
1577 class PathMapTileEdge(IMP._Value):
1578  r"""Proxy of C++ IMP::bff::PathMapTileEdge class."""
1579 
1580  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1581 
1582  def get_length(self):
1583  r"""get_length(PathMapTileEdge self) -> float"""
1584  return _IMP_bff.PathMapTileEdge_get_length(self)
1585 
1586  def __init__(self, *args, **kwargs):
1587  r"""__init__(PathMapTileEdge self, int edge_target=-1, float edge_cost=std::numeric_limits< float >::max()) -> PathMapTileEdge"""
1588  _IMP_bff.PathMapTileEdge_swiginit(self, _IMP_bff.new_PathMapTileEdge(*args, **kwargs))
1589 
1590  def show(self, *args, **kwargs):
1591  r"""show(PathMapTileEdge self, _ostream out=std::cout)"""
1592  return _IMP_bff.PathMapTileEdge_show(self, *args, **kwargs)
1593 
1594  def __str__(self):
1595  r"""__str__(PathMapTileEdge self) -> std::string"""
1596  return _IMP_bff.PathMapTileEdge___str__(self)
1597 
1598  def __repr__(self):
1599  r"""__repr__(PathMapTileEdge self) -> std::string"""
1600  return _IMP_bff.PathMapTileEdge___repr__(self)
1601  __swig_destroy__ = _IMP_bff.delete_PathMapTileEdge
1602 
1603 # Register PathMapTileEdge in _IMP_bff:
1604 _IMP_bff.PathMapTileEdge_swigregister(PathMapTileEdge)
1605 class VectorPathMapTile(object):
1606  r"""Proxy of C++ std::vector< IMP::bff::PathMapTile > class."""
1607 
1608  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1609  __repr__ = _swig_repr
1610 
1611  def iterator(self):
1612  r"""iterator(VectorPathMapTile self) -> IMP_BFF_SwigPyIterator"""
1613  return _IMP_bff.VectorPathMapTile_iterator(self)
1614  def __iter__(self):
1615  return self.iterator()
1616 
1617  def __nonzero__(self):
1618  r"""__nonzero__(VectorPathMapTile self) -> bool"""
1619  return _IMP_bff.VectorPathMapTile___nonzero__(self)
1620 
1621  def __bool__(self):
1622  r"""__bool__(VectorPathMapTile self) -> bool"""
1623  return _IMP_bff.VectorPathMapTile___bool__(self)
1624 
1625  def __len__(self):
1626  r"""__len__(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::size_type"""
1627  return _IMP_bff.VectorPathMapTile___len__(self)
1628 
1629  def __getslice__(self, i, j):
1630  r"""__getslice__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i, std::vector< IMP::bff::PathMapTile >::difference_type j) -> VectorPathMapTile"""
1631  return _IMP_bff.VectorPathMapTile___getslice__(self, i, j)
1632 
1633  def __setslice__(self, *args):
1634  r"""
1635  __setslice__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i, std::vector< IMP::bff::PathMapTile >::difference_type j)
1636  __setslice__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i, std::vector< IMP::bff::PathMapTile >::difference_type j, VectorPathMapTile v)
1637  """
1638  return _IMP_bff.VectorPathMapTile___setslice__(self, *args)
1639 
1640  def __delslice__(self, i, j):
1641  r"""__delslice__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i, std::vector< IMP::bff::PathMapTile >::difference_type j)"""
1642  return _IMP_bff.VectorPathMapTile___delslice__(self, i, j)
1643 
1644  def __delitem__(self, *args):
1645  r"""
1646  __delitem__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i)
1647  __delitem__(VectorPathMapTile self, SWIGPY_SLICEOBJECT * slice)
1648  """
1649  return _IMP_bff.VectorPathMapTile___delitem__(self, *args)
1650 
1651  def __getitem__(self, *args):
1652  r"""
1653  __getitem__(VectorPathMapTile self, SWIGPY_SLICEOBJECT * slice) -> VectorPathMapTile
1654  __getitem__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i) -> PathMapTile
1655  """
1656  return _IMP_bff.VectorPathMapTile___getitem__(self, *args)
1657 
1658  def __setitem__(self, *args):
1659  r"""
1660  __setitem__(VectorPathMapTile self, SWIGPY_SLICEOBJECT * slice, VectorPathMapTile v)
1661  __setitem__(VectorPathMapTile self, SWIGPY_SLICEOBJECT * slice)
1662  __setitem__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::difference_type i, PathMapTile x)
1663  """
1664  return _IMP_bff.VectorPathMapTile___setitem__(self, *args)
1665 
1666  def pop(self):
1667  r"""pop(VectorPathMapTile self) -> PathMapTile"""
1668  return _IMP_bff.VectorPathMapTile_pop(self)
1669 
1670  def append(self, x):
1671  r"""append(VectorPathMapTile self, PathMapTile x)"""
1672  return _IMP_bff.VectorPathMapTile_append(self, x)
1673 
1674  def empty(self):
1675  r"""empty(VectorPathMapTile self) -> bool"""
1676  return _IMP_bff.VectorPathMapTile_empty(self)
1677 
1678  def size(self):
1679  r"""size(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::size_type"""
1680  return _IMP_bff.VectorPathMapTile_size(self)
1681 
1682  def swap(self, v):
1683  r"""swap(VectorPathMapTile self, VectorPathMapTile v)"""
1684  return _IMP_bff.VectorPathMapTile_swap(self, v)
1685 
1686  def begin(self):
1687  r"""begin(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::iterator"""
1688  return _IMP_bff.VectorPathMapTile_begin(self)
1689 
1690  def end(self):
1691  r"""end(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::iterator"""
1692  return _IMP_bff.VectorPathMapTile_end(self)
1693 
1694  def rbegin(self):
1695  r"""rbegin(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::reverse_iterator"""
1696  return _IMP_bff.VectorPathMapTile_rbegin(self)
1697 
1698  def rend(self):
1699  r"""rend(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::reverse_iterator"""
1700  return _IMP_bff.VectorPathMapTile_rend(self)
1701 
1702  def clear(self):
1703  r"""clear(VectorPathMapTile self)"""
1704  return _IMP_bff.VectorPathMapTile_clear(self)
1705 
1706  def get_allocator(self):
1707  r"""get_allocator(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::allocator_type"""
1708  return _IMP_bff.VectorPathMapTile_get_allocator(self)
1709 
1710  def pop_back(self):
1711  r"""pop_back(VectorPathMapTile self)"""
1712  return _IMP_bff.VectorPathMapTile_pop_back(self)
1713 
1714  def erase(self, *args):
1715  r"""
1716  erase(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::iterator pos) -> std::vector< IMP::bff::PathMapTile >::iterator
1717  erase(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::iterator first, std::vector< IMP::bff::PathMapTile >::iterator last) -> std::vector< IMP::bff::PathMapTile >::iterator
1718  """
1719  return _IMP_bff.VectorPathMapTile_erase(self, *args)
1720 
1721  def __init__(self, *args):
1722  r"""
1723  __init__(VectorPathMapTile self) -> VectorPathMapTile
1724  __init__(VectorPathMapTile self, VectorPathMapTile other) -> VectorPathMapTile
1725  __init__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type size) -> VectorPathMapTile
1726  __init__(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type size, PathMapTile value) -> VectorPathMapTile
1727  """
1728  _IMP_bff.VectorPathMapTile_swiginit(self, _IMP_bff.new_VectorPathMapTile(*args))
1729 
1730  def push_back(self, x):
1731  r"""push_back(VectorPathMapTile self, PathMapTile x)"""
1732  return _IMP_bff.VectorPathMapTile_push_back(self, x)
1733 
1734  def front(self):
1735  r"""front(VectorPathMapTile self) -> PathMapTile"""
1736  return _IMP_bff.VectorPathMapTile_front(self)
1737 
1738  def back(self):
1739  r"""back(VectorPathMapTile self) -> PathMapTile"""
1740  return _IMP_bff.VectorPathMapTile_back(self)
1741 
1742  def assign(self, n, x):
1743  r"""assign(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type n, PathMapTile x)"""
1744  return _IMP_bff.VectorPathMapTile_assign(self, n, x)
1745 
1746  def resize(self, *args):
1747  r"""
1748  resize(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type new_size)
1749  resize(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type new_size, PathMapTile x)
1750  """
1751  return _IMP_bff.VectorPathMapTile_resize(self, *args)
1752 
1753  def insert(self, *args):
1754  r"""
1755  insert(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::iterator pos, PathMapTile x) -> std::vector< IMP::bff::PathMapTile >::iterator
1756  insert(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::iterator pos, std::vector< IMP::bff::PathMapTile >::size_type n, PathMapTile x)
1757  """
1758  return _IMP_bff.VectorPathMapTile_insert(self, *args)
1759 
1760  def reserve(self, n):
1761  r"""reserve(VectorPathMapTile self, std::vector< IMP::bff::PathMapTile >::size_type n)"""
1762  return _IMP_bff.VectorPathMapTile_reserve(self, n)
1763 
1764  def capacity(self):
1765  r"""capacity(VectorPathMapTile self) -> std::vector< IMP::bff::PathMapTile >::size_type"""
1766  return _IMP_bff.VectorPathMapTile_capacity(self)
1767  __swig_destroy__ = _IMP_bff.delete_VectorPathMapTile
1768 
1769 # Register VectorPathMapTile in _IMP_bff:
1770 _IMP_bff.VectorPathMapTile_swigregister(VectorPathMapTile)
1771 class VectorPathMapTileEdge(object):
1772  r"""Proxy of C++ std::vector< IMP::bff::PathMapTileEdge > class."""
1773 
1774  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1775  __repr__ = _swig_repr
1776 
1777  def iterator(self):
1778  r"""iterator(VectorPathMapTileEdge self) -> IMP_BFF_SwigPyIterator"""
1779  return _IMP_bff.VectorPathMapTileEdge_iterator(self)
1780  def __iter__(self):
1781  return self.iterator()
1782 
1783  def __nonzero__(self):
1784  r"""__nonzero__(VectorPathMapTileEdge self) -> bool"""
1785  return _IMP_bff.VectorPathMapTileEdge___nonzero__(self)
1786 
1787  def __bool__(self):
1788  r"""__bool__(VectorPathMapTileEdge self) -> bool"""
1789  return _IMP_bff.VectorPathMapTileEdge___bool__(self)
1790 
1791  def __len__(self):
1792  r"""__len__(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::size_type"""
1793  return _IMP_bff.VectorPathMapTileEdge___len__(self)
1794 
1795  def __getslice__(self, i, j):
1796  r"""__getslice__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i, std::vector< IMP::bff::PathMapTileEdge >::difference_type j) -> VectorPathMapTileEdge"""
1797  return _IMP_bff.VectorPathMapTileEdge___getslice__(self, i, j)
1798 
1799  def __setslice__(self, *args):
1800  r"""
1801  __setslice__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i, std::vector< IMP::bff::PathMapTileEdge >::difference_type j)
1802  __setslice__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i, std::vector< IMP::bff::PathMapTileEdge >::difference_type j, VectorPathMapTileEdge v)
1803  """
1804  return _IMP_bff.VectorPathMapTileEdge___setslice__(self, *args)
1805 
1806  def __delslice__(self, i, j):
1807  r"""__delslice__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i, std::vector< IMP::bff::PathMapTileEdge >::difference_type j)"""
1808  return _IMP_bff.VectorPathMapTileEdge___delslice__(self, i, j)
1809 
1810  def __delitem__(self, *args):
1811  r"""
1812  __delitem__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i)
1813  __delitem__(VectorPathMapTileEdge self, SWIGPY_SLICEOBJECT * slice)
1814  """
1815  return _IMP_bff.VectorPathMapTileEdge___delitem__(self, *args)
1816 
1817  def __getitem__(self, *args):
1818  r"""
1819  __getitem__(VectorPathMapTileEdge self, SWIGPY_SLICEOBJECT * slice) -> VectorPathMapTileEdge
1820  __getitem__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i) -> PathMapTileEdge
1821  """
1822  return _IMP_bff.VectorPathMapTileEdge___getitem__(self, *args)
1823 
1824  def __setitem__(self, *args):
1825  r"""
1826  __setitem__(VectorPathMapTileEdge self, SWIGPY_SLICEOBJECT * slice, VectorPathMapTileEdge v)
1827  __setitem__(VectorPathMapTileEdge self, SWIGPY_SLICEOBJECT * slice)
1828  __setitem__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::difference_type i, PathMapTileEdge x)
1829  """
1830  return _IMP_bff.VectorPathMapTileEdge___setitem__(self, *args)
1831 
1832  def pop(self):
1833  r"""pop(VectorPathMapTileEdge self) -> PathMapTileEdge"""
1834  return _IMP_bff.VectorPathMapTileEdge_pop(self)
1835 
1836  def append(self, x):
1837  r"""append(VectorPathMapTileEdge self, PathMapTileEdge x)"""
1838  return _IMP_bff.VectorPathMapTileEdge_append(self, x)
1839 
1840  def empty(self):
1841  r"""empty(VectorPathMapTileEdge self) -> bool"""
1842  return _IMP_bff.VectorPathMapTileEdge_empty(self)
1843 
1844  def size(self):
1845  r"""size(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::size_type"""
1846  return _IMP_bff.VectorPathMapTileEdge_size(self)
1847 
1848  def swap(self, v):
1849  r"""swap(VectorPathMapTileEdge self, VectorPathMapTileEdge v)"""
1850  return _IMP_bff.VectorPathMapTileEdge_swap(self, v)
1851 
1852  def begin(self):
1853  r"""begin(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::iterator"""
1854  return _IMP_bff.VectorPathMapTileEdge_begin(self)
1855 
1856  def end(self):
1857  r"""end(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::iterator"""
1858  return _IMP_bff.VectorPathMapTileEdge_end(self)
1859 
1860  def rbegin(self):
1861  r"""rbegin(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::reverse_iterator"""
1862  return _IMP_bff.VectorPathMapTileEdge_rbegin(self)
1863 
1864  def rend(self):
1865  r"""rend(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::reverse_iterator"""
1866  return _IMP_bff.VectorPathMapTileEdge_rend(self)
1867 
1868  def clear(self):
1869  r"""clear(VectorPathMapTileEdge self)"""
1870  return _IMP_bff.VectorPathMapTileEdge_clear(self)
1871 
1872  def get_allocator(self):
1873  r"""get_allocator(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::allocator_type"""
1874  return _IMP_bff.VectorPathMapTileEdge_get_allocator(self)
1875 
1876  def pop_back(self):
1877  r"""pop_back(VectorPathMapTileEdge self)"""
1878  return _IMP_bff.VectorPathMapTileEdge_pop_back(self)
1879 
1880  def erase(self, *args):
1881  r"""
1882  erase(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::iterator pos) -> std::vector< IMP::bff::PathMapTileEdge >::iterator
1883  erase(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::iterator first, std::vector< IMP::bff::PathMapTileEdge >::iterator last) -> std::vector< IMP::bff::PathMapTileEdge >::iterator
1884  """
1885  return _IMP_bff.VectorPathMapTileEdge_erase(self, *args)
1886 
1887  def __init__(self, *args):
1888  r"""
1889  __init__(VectorPathMapTileEdge self) -> VectorPathMapTileEdge
1890  __init__(VectorPathMapTileEdge self, VectorPathMapTileEdge other) -> VectorPathMapTileEdge
1891  __init__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type size) -> VectorPathMapTileEdge
1892  __init__(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type size, PathMapTileEdge value) -> VectorPathMapTileEdge
1893  """
1894  _IMP_bff.VectorPathMapTileEdge_swiginit(self, _IMP_bff.new_VectorPathMapTileEdge(*args))
1895 
1896  def push_back(self, x):
1897  r"""push_back(VectorPathMapTileEdge self, PathMapTileEdge x)"""
1898  return _IMP_bff.VectorPathMapTileEdge_push_back(self, x)
1899 
1900  def front(self):
1901  r"""front(VectorPathMapTileEdge self) -> PathMapTileEdge"""
1902  return _IMP_bff.VectorPathMapTileEdge_front(self)
1903 
1904  def back(self):
1905  r"""back(VectorPathMapTileEdge self) -> PathMapTileEdge"""
1906  return _IMP_bff.VectorPathMapTileEdge_back(self)
1907 
1908  def assign(self, n, x):
1909  r"""assign(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type n, PathMapTileEdge x)"""
1910  return _IMP_bff.VectorPathMapTileEdge_assign(self, n, x)
1911 
1912  def resize(self, *args):
1913  r"""
1914  resize(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type new_size)
1915  resize(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type new_size, PathMapTileEdge x)
1916  """
1917  return _IMP_bff.VectorPathMapTileEdge_resize(self, *args)
1918 
1919  def insert(self, *args):
1920  r"""
1921  insert(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::iterator pos, PathMapTileEdge x) -> std::vector< IMP::bff::PathMapTileEdge >::iterator
1922  insert(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::iterator pos, std::vector< IMP::bff::PathMapTileEdge >::size_type n, PathMapTileEdge x)
1923  """
1924  return _IMP_bff.VectorPathMapTileEdge_insert(self, *args)
1925 
1926  def reserve(self, n):
1927  r"""reserve(VectorPathMapTileEdge self, std::vector< IMP::bff::PathMapTileEdge >::size_type n)"""
1928  return _IMP_bff.VectorPathMapTileEdge_reserve(self, n)
1929 
1930  def capacity(self):
1931  r"""capacity(VectorPathMapTileEdge self) -> std::vector< IMP::bff::PathMapTileEdge >::size_type"""
1932  return _IMP_bff.VectorPathMapTileEdge_capacity(self)
1933  __swig_destroy__ = _IMP_bff.delete_VectorPathMapTileEdge
1934 
1935 # Register VectorPathMapTileEdge in _IMP_bff:
1936 _IMP_bff.VectorPathMapTileEdge_swigregister(VectorPathMapTileEdge)
1937 
1938 def AVs(l=[]):
1939  return [AV(x) for x in l]
1940 _plural_types.append("AVs")
1941 
1942 
1943 _value_types.append("AV")
1944 
1945 
1946 AVPairDistanceMeasurements=list
1947 _plural_types.append("AVPairDistanceMeasurements")
1948 _value_types.append("AVPairDistanceMeasurement")
1949 
1950 
1951 _object_types.append("AVNetworkRestraint")
1952 
1953 
1954 def _object_cast_to_AVNetworkRestraint(o):
1955  r"""_object_cast_to_AVNetworkRestraint(Object o) -> AVNetworkRestraint"""
1956  return _IMP_bff._object_cast_to_AVNetworkRestraint(o)
1957 class MapStringAVPairDistanceMeasurement(object):
1958  r"""Proxy of C++ std::map< std::string,IMP::bff::AVPairDistanceMeasurement > class."""
1959 
1960  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1961  __repr__ = _swig_repr
1962 
1963  def iterator(self):
1964  r"""iterator(MapStringAVPairDistanceMeasurement self) -> IMP_BFF_SwigPyIterator"""
1965  return _IMP_bff.MapStringAVPairDistanceMeasurement_iterator(self)
1966  def __iter__(self):
1967  return self.iterator()
1968 
1969  def __nonzero__(self):
1970  r"""__nonzero__(MapStringAVPairDistanceMeasurement self) -> bool"""
1971  return _IMP_bff.MapStringAVPairDistanceMeasurement___nonzero__(self)
1972 
1973  def __bool__(self):
1974  r"""__bool__(MapStringAVPairDistanceMeasurement self) -> bool"""
1975  return _IMP_bff.MapStringAVPairDistanceMeasurement___bool__(self)
1976 
1977  def __len__(self):
1978  r"""__len__(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::size_type"""
1979  return _IMP_bff.MapStringAVPairDistanceMeasurement___len__(self)
1980  def __iter__(self):
1981  return self.key_iterator()
1982  def iterkeys(self):
1983  return self.key_iterator()
1984  def itervalues(self):
1985  return self.value_iterator()
1986  def iteritems(self):
1987  return self.iterator()
1988 
1989  def __getitem__(self, key):
1990  r"""__getitem__(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key) -> AVPairDistanceMeasurement"""
1991  return _IMP_bff.MapStringAVPairDistanceMeasurement___getitem__(self, key)
1992 
1993  def __delitem__(self, key):
1994  r"""__delitem__(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key)"""
1995  return _IMP_bff.MapStringAVPairDistanceMeasurement___delitem__(self, key)
1996 
1997  def has_key(self, key):
1998  r"""has_key(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key) -> bool"""
1999  return _IMP_bff.MapStringAVPairDistanceMeasurement_has_key(self, key)
2000 
2001  def keys(self):
2002  r"""keys(MapStringAVPairDistanceMeasurement self) -> PyObject *"""
2003  return _IMP_bff.MapStringAVPairDistanceMeasurement_keys(self)
2004 
2005  def values(self):
2006  r"""values(MapStringAVPairDistanceMeasurement self) -> PyObject *"""
2007  return _IMP_bff.MapStringAVPairDistanceMeasurement_values(self)
2008 
2009  def items(self):
2010  r"""items(MapStringAVPairDistanceMeasurement self) -> PyObject *"""
2011  return _IMP_bff.MapStringAVPairDistanceMeasurement_items(self)
2012 
2013  def __contains__(self, key):
2014  r"""__contains__(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key) -> bool"""
2015  return _IMP_bff.MapStringAVPairDistanceMeasurement___contains__(self, key)
2016 
2017  def key_iterator(self):
2018  r"""key_iterator(MapStringAVPairDistanceMeasurement self) -> IMP_BFF_SwigPyIterator"""
2019  return _IMP_bff.MapStringAVPairDistanceMeasurement_key_iterator(self)
2020 
2021  def value_iterator(self):
2022  r"""value_iterator(MapStringAVPairDistanceMeasurement self) -> IMP_BFF_SwigPyIterator"""
2023  return _IMP_bff.MapStringAVPairDistanceMeasurement_value_iterator(self)
2024 
2025  def __setitem__(self, *args):
2026  r"""
2027  __setitem__(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key)
2028  __setitem__(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & key, AVPairDistanceMeasurement x)
2029  """
2030  return _IMP_bff.MapStringAVPairDistanceMeasurement___setitem__(self, *args)
2031 
2032  def asdict(self):
2033  r"""asdict(MapStringAVPairDistanceMeasurement self) -> PyObject *"""
2034  return _IMP_bff.MapStringAVPairDistanceMeasurement_asdict(self)
2035 
2036  def __init__(self, *args):
2037  r"""
2038  __init__(MapStringAVPairDistanceMeasurement self, std::less< std::string > const & other) -> MapStringAVPairDistanceMeasurement
2039  __init__(MapStringAVPairDistanceMeasurement self) -> MapStringAVPairDistanceMeasurement
2040  __init__(MapStringAVPairDistanceMeasurement self, MapStringAVPairDistanceMeasurement other) -> MapStringAVPairDistanceMeasurement
2041  """
2042  _IMP_bff.MapStringAVPairDistanceMeasurement_swiginit(self, _IMP_bff.new_MapStringAVPairDistanceMeasurement(*args))
2043 
2044  def empty(self):
2045  r"""empty(MapStringAVPairDistanceMeasurement self) -> bool"""
2046  return _IMP_bff.MapStringAVPairDistanceMeasurement_empty(self)
2047 
2048  def size(self):
2049  r"""size(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::size_type"""
2050  return _IMP_bff.MapStringAVPairDistanceMeasurement_size(self)
2051 
2052  def swap(self, v):
2053  r"""swap(MapStringAVPairDistanceMeasurement self, MapStringAVPairDistanceMeasurement v)"""
2054  return _IMP_bff.MapStringAVPairDistanceMeasurement_swap(self, v)
2055 
2056  def begin(self):
2057  r"""begin(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator"""
2058  return _IMP_bff.MapStringAVPairDistanceMeasurement_begin(self)
2059 
2060  def end(self):
2061  r"""end(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator"""
2062  return _IMP_bff.MapStringAVPairDistanceMeasurement_end(self)
2063 
2064  def rbegin(self):
2065  r"""rbegin(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::reverse_iterator"""
2066  return _IMP_bff.MapStringAVPairDistanceMeasurement_rbegin(self)
2067 
2068  def rend(self):
2069  r"""rend(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::reverse_iterator"""
2070  return _IMP_bff.MapStringAVPairDistanceMeasurement_rend(self)
2071 
2072  def clear(self):
2073  r"""clear(MapStringAVPairDistanceMeasurement self)"""
2074  return _IMP_bff.MapStringAVPairDistanceMeasurement_clear(self)
2075 
2076  def get_allocator(self):
2077  r"""get_allocator(MapStringAVPairDistanceMeasurement self) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::allocator_type"""
2078  return _IMP_bff.MapStringAVPairDistanceMeasurement_get_allocator(self)
2079 
2080  def count(self, x):
2081  r"""count(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & x) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::size_type"""
2082  return _IMP_bff.MapStringAVPairDistanceMeasurement_count(self, x)
2083 
2084  def erase(self, *args):
2085  r"""
2086  erase(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & x) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::size_type
2087  erase(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator position)
2088  erase(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator first, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator last)
2089  """
2090  return _IMP_bff.MapStringAVPairDistanceMeasurement_erase(self, *args)
2091 
2092  def find(self, x):
2093  r"""find(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & x) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator"""
2094  return _IMP_bff.MapStringAVPairDistanceMeasurement_find(self, x)
2095 
2096  def lower_bound(self, x):
2097  r"""lower_bound(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & x) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator"""
2098  return _IMP_bff.MapStringAVPairDistanceMeasurement_lower_bound(self, x)
2099 
2100  def upper_bound(self, x):
2101  r"""upper_bound(MapStringAVPairDistanceMeasurement self, std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::key_type const & x) -> std::map< std::string,IMP::bff::AVPairDistanceMeasurement >::iterator"""
2102  return _IMP_bff.MapStringAVPairDistanceMeasurement_upper_bound(self, x)
2103  __swig_destroy__ = _IMP_bff.delete_MapStringAVPairDistanceMeasurement
2104 
2105 # Register MapStringAVPairDistanceMeasurement in _IMP_bff:
2106 _IMP_bff.MapStringAVPairDistanceMeasurement_swigregister(MapStringAVPairDistanceMeasurement)
2107 DYE_PAIR_DISTANCE_E = _IMP_bff.DYE_PAIR_DISTANCE_E
2108 
2109 DYE_PAIR_DISTANCE_MEAN = _IMP_bff.DYE_PAIR_DISTANCE_MEAN
2110 
2111 DYE_PAIR_DISTANCE_MP = _IMP_bff.DYE_PAIR_DISTANCE_MP
2112 
2113 DYE_PAIR_EFFICIENCY = _IMP_bff.DYE_PAIR_EFFICIENCY
2114 
2115 DYE_PAIR_DISTANCE_DISTRIBUTION = _IMP_bff.DYE_PAIR_DISTANCE_DISTRIBUTION
2116 
2117 DYE_PAIR_XYZ_DISTANCE = _IMP_bff.DYE_PAIR_XYZ_DISTANCE
2118 
2119 class AVPairDistanceMeasurement(IMP._Value):
2120  r"""Proxy of C++ IMP::bff::AVPairDistanceMeasurement class."""
2121 
2122  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2123  distance = property(_IMP_bff.AVPairDistanceMeasurement_distance_get, _IMP_bff.AVPairDistanceMeasurement_distance_set, doc=r"""distance : double""")
2124  error_neg = property(_IMP_bff.AVPairDistanceMeasurement_error_neg_get, _IMP_bff.AVPairDistanceMeasurement_error_neg_set, doc=r"""error_neg : double""")
2125  error_pos = property(_IMP_bff.AVPairDistanceMeasurement_error_pos_get, _IMP_bff.AVPairDistanceMeasurement_error_pos_set, doc=r"""error_pos : double""")
2126  forster_radius = property(_IMP_bff.AVPairDistanceMeasurement_forster_radius_get, _IMP_bff.AVPairDistanceMeasurement_forster_radius_set, doc=r"""forster_radius : double""")
2127  distance_type = property(_IMP_bff.AVPairDistanceMeasurement_distance_type_get, _IMP_bff.AVPairDistanceMeasurement_distance_type_set, doc=r"""distance_type : int""")
2128  position_1 = property(_IMP_bff.AVPairDistanceMeasurement_position_1_get, _IMP_bff.AVPairDistanceMeasurement_position_1_set, doc=r"""position_1 : std::string""")
2129  position_2 = property(_IMP_bff.AVPairDistanceMeasurement_position_2_get, _IMP_bff.AVPairDistanceMeasurement_position_2_set, doc=r"""position_2 : std::string""")
2130 
2131  def get_json(self):
2132  r"""get_json(AVPairDistanceMeasurement self) -> std::string"""
2133  return _IMP_bff.AVPairDistanceMeasurement_get_json(self)
2134 
2135  def score_model(self, model):
2136  r"""score_model(AVPairDistanceMeasurement self, double model) -> double"""
2137  return _IMP_bff.AVPairDistanceMeasurement_score_model(self, model)
2138 
2139  def show(self, *args, **kwargs):
2140  r"""show(AVPairDistanceMeasurement self, _ostream out=std::cout)"""
2141  return _IMP_bff.AVPairDistanceMeasurement_show(self, *args, **kwargs)
2142 
2143  def __str__(self):
2144  r"""__str__(AVPairDistanceMeasurement self) -> std::string"""
2145  return _IMP_bff.AVPairDistanceMeasurement___str__(self)
2146 
2147  def __repr__(self):
2148  r"""__repr__(AVPairDistanceMeasurement self) -> std::string"""
2149  return _IMP_bff.AVPairDistanceMeasurement___repr__(self)
2150 
2151  def __init__(self):
2152  r"""__init__(AVPairDistanceMeasurement self) -> AVPairDistanceMeasurement"""
2153  _IMP_bff.AVPairDistanceMeasurement_swiginit(self, _IMP_bff.new_AVPairDistanceMeasurement())
2154  __swig_destroy__ = _IMP_bff.delete_AVPairDistanceMeasurement
2155 
2156 # Register AVPairDistanceMeasurement in _IMP_bff:
2157 _IMP_bff.AVPairDistanceMeasurement_swigregister(AVPairDistanceMeasurement)
2158 class AV(IMP.core.Gaussian):
2159  r"""Proxy of C++ IMP::bff::AV class."""
2160 
2161  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2162 
2163  def create_path_map_header(self):
2164  r"""create_path_map_header(AV self) -> PathMapHeader"""
2165  return _IMP_bff.AV_create_path_map_header(self)
2166 
2167  def init_path_map(self):
2168  r"""init_path_map(AV self)"""
2169  return _IMP_bff.AV_init_path_map(self)
2170 
2171  @staticmethod
2172  def get_av_key(i):
2173  r"""get_av_key(unsigned int i) -> FloatKey"""
2174  return _IMP_bff.AV_get_av_key(i)
2175 
2176  @staticmethod
2177  def do_setup_particle(*args, **kwargs):
2178  r"""do_setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_source, double linker_length=20.0, Vector3D radii=IMP::algebra::Vector3D(3.5, 0, 0), double linker_width=0.5, double allowed_sphere_radius=1.5, double contact_volume_thickness=0.0, double contact_volume_trapped_fraction=-1, double simulation_grid_resolution=1.5)"""
2179  return _IMP_bff.AV_do_setup_particle(*args, **kwargs)
2180 
2181  @staticmethod
2182  def get_particle_key(i):
2183  r"""get_particle_key(unsigned int i) -> ParticleIndexKey"""
2184  return _IMP_bff.AV_get_particle_key(i)
2185 
2186  def get_particle_index(self, *args):
2187  r"""
2188  get_particle_index(AV self) -> ParticleIndex
2189  get_particle_index(AV self, unsigned int i) -> ParticleIndex
2190  """
2191  return _IMP_bff.AV_get_particle_index(self, *args)
2192 
2193  def get_particle(self, *args):
2194  r"""
2195  get_particle(AV self) -> Particle
2196  get_particle(AV self, unsigned int i) -> Particle
2197  """
2198  return _IMP_bff.AV_get_particle(self, *args)
2199 
2200  def __init__(self, *args):
2201  r"""
2202  __init__(AV self) -> AV
2203  __init__(AV self, Model m, ParticleIndex id) -> AV
2204  __init__(AV self, _ParticleAdaptor d) -> AV
2205  """
2206  _IMP_bff.AV_swiginit(self, _IMP_bff.new_AV(*args))
2207 
2208  def show(self, *args, **kwargs):
2209  r"""show(AV self, _ostream out=std::cout)"""
2210  return _IMP_bff.AV_show(self, *args, **kwargs)
2211 
2212  @staticmethod
2213  def setup_particle(*args):
2214  r"""
2215  setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_source) -> AV
2216  setup_particle(_ParticleAdaptor pa, ParticleIndex pi_source) -> AV
2217  """
2218  return _IMP_bff.AV_setup_particle(*args)
2219 
2220  def get_linker_length(self):
2221  r"""get_linker_length(AV self) -> IMP::Float"""
2222  return _IMP_bff.AV_get_linker_length(self)
2223 
2224  def set_linker_length(self, t):
2225  r"""set_linker_length(AV self, IMP::Float t)"""
2226  return _IMP_bff.AV_set_linker_length(self, t)
2227 
2228  def get_radius1(self):
2229  r"""get_radius1(AV self) -> IMP::Float"""
2230  return _IMP_bff.AV_get_radius1(self)
2231 
2232  def set_radius1(self, t):
2233  r"""set_radius1(AV self, IMP::Float t)"""
2234  return _IMP_bff.AV_set_radius1(self, t)
2235 
2236  def get_radius2(self):
2237  r"""get_radius2(AV self) -> IMP::Float"""
2238  return _IMP_bff.AV_get_radius2(self)
2239 
2240  def set_radius2(self, t):
2241  r"""set_radius2(AV self, IMP::Float t)"""
2242  return _IMP_bff.AV_set_radius2(self, t)
2243 
2244  def get_radius3(self):
2245  r"""get_radius3(AV self) -> IMP::Float"""
2246  return _IMP_bff.AV_get_radius3(self)
2247 
2248  def set_radius3(self, t):
2249  r"""set_radius3(AV self, IMP::Float t)"""
2250  return _IMP_bff.AV_set_radius3(self, t)
2251 
2252  def get_linker_width(self):
2253  r"""get_linker_width(AV self) -> IMP::Float"""
2254  return _IMP_bff.AV_get_linker_width(self)
2255 
2256  def set_linker_width(self, t):
2257  r"""set_linker_width(AV self, IMP::Float t)"""
2258  return _IMP_bff.AV_set_linker_width(self, t)
2259 
2260  def get_allowed_sphere_radius(self):
2261  r"""get_allowed_sphere_radius(AV self) -> IMP::Float"""
2262  return _IMP_bff.AV_get_allowed_sphere_radius(self)
2263 
2264  def set_allowed_sphere_radius(self, t):
2265  r"""set_allowed_sphere_radius(AV self, IMP::Float t)"""
2266  return _IMP_bff.AV_set_allowed_sphere_radius(self, t)
2267 
2268  def get_contact_volume_thickness(self):
2269  r"""get_contact_volume_thickness(AV self) -> IMP::Float"""
2270  return _IMP_bff.AV_get_contact_volume_thickness(self)
2271 
2272  def set_contact_volume_thickness(self, t):
2273  r"""set_contact_volume_thickness(AV self, IMP::Float t)"""
2274  return _IMP_bff.AV_set_contact_volume_thickness(self, t)
2275 
2276  def get_contact_volume_trapped_fraction(self):
2277  r"""get_contact_volume_trapped_fraction(AV self) -> IMP::Float"""
2278  return _IMP_bff.AV_get_contact_volume_trapped_fraction(self)
2279 
2280  def set_contact_volume_trapped_fraction(self, t):
2281  r"""set_contact_volume_trapped_fraction(AV self, IMP::Float t)"""
2282  return _IMP_bff.AV_set_contact_volume_trapped_fraction(self, t)
2283 
2284  def get_simulation_grid_resolution(self):
2285  r"""get_simulation_grid_resolution(AV self) -> IMP::Float"""
2286  return _IMP_bff.AV_get_simulation_grid_resolution(self)
2287 
2288  def set_simulation_grid_resolution(self, t):
2289  r"""set_simulation_grid_resolution(AV self, IMP::Float t)"""
2290  return _IMP_bff.AV_set_simulation_grid_resolution(self, t)
2291 
2292  def get_radii(self):
2293  r"""get_radii(AV self) -> Vector3D"""
2294  return _IMP_bff.AV_get_radii(self)
2295 
2296  def get_parameters_are_optimized(self):
2297  r"""get_parameters_are_optimized(AV self) -> bool"""
2298  return _IMP_bff.AV_get_parameters_are_optimized(self)
2299 
2300  def set_av_parameters_are_optimized(self, tf):
2301  r"""set_av_parameters_are_optimized(AV self, bool tf)"""
2302  return _IMP_bff.AV_set_av_parameters_are_optimized(self, tf)
2303 
2304  def set_av_parameter(self, j):
2305  r"""set_av_parameter(AV self, nlohmann::json const & j)"""
2306  return _IMP_bff.AV_set_av_parameter(self, j)
2307 
2308  def get_derivatives(self):
2309  r"""get_derivatives(AV self) -> Vector3D"""
2310  return _IMP_bff.AV_get_derivatives(self)
2311 
2312  @staticmethod
2313  def get_is_setup(*args):
2314  r"""
2315  get_is_setup(_ParticleAdaptor p) -> bool
2316  get_is_setup(Model m, ParticleIndex pi) -> bool
2317  """
2318  return _IMP_bff.AV_get_is_setup(*args)
2319 
2320  def get_map(self):
2321  r"""get_map(AV self) -> PathMap"""
2322  return _IMP_bff.AV_get_map(self)
2323 
2324  def resample(self, shift_xyz=True):
2325  r"""resample(AV self, bool shift_xyz=True)"""
2326  return _IMP_bff.AV_resample(self, shift_xyz)
2327 
2328  def get_mean_position(self, include_source=True):
2329  r"""get_mean_position(AV self, bool include_source=True) -> Vector3D"""
2330  return _IMP_bff.AV_get_mean_position(self, include_source)
2331 
2332  def get_source_coordinates(self):
2333  r"""get_source_coordinates(AV self) -> Vector3D"""
2334  return _IMP_bff.AV_get_source_coordinates(self)
2335 
2336  def get_source(self):
2337  r"""get_source(AV self) -> Particle"""
2338  return _IMP_bff.AV_get_source(self)
2339 
2340  def add_attribute(self, *args):
2341  r"""
2342  add_attribute(AV self, FloatKey k, IMP::Float v, bool opt)
2343  add_attribute(AV self, FloatKey a0, IMP::Float a1)
2344  add_attribute(AV self, IntKey a0, IMP::Int a1)
2345  add_attribute(AV self, FloatsKey a0, IMP::Floats a1)
2346  add_attribute(AV self, IntsKey a0, IMP::Ints a1)
2347  add_attribute(AV self, StringKey a0, IMP::String a1)
2348  add_attribute(AV self, ParticleIndexKey a0, Particle a1)
2349  add_attribute(AV self, ObjectKey a0, Object a1)
2350  add_attribute(AV self, SparseFloatKey a0, IMP::Float a1)
2351  add_attribute(AV self, SparseIntKey a0, IMP::Int a1)
2352  add_attribute(AV self, SparseStringKey a0, IMP::String a1)
2353  add_attribute(AV self, SparseParticleIndexKey a0, ParticleIndex a1)
2354  """
2355  return _IMP_bff.AV_add_attribute(self, *args)
2356 
2357  def get_value(self, *args):
2358  r"""
2359  get_value(AV self, FloatKey a0) -> IMP::Float
2360  get_value(AV self, IntKey a0) -> IMP::Int
2361  get_value(AV self, FloatsKey a0) -> IMP::Floats
2362  get_value(AV self, IntsKey a0) -> IMP::Ints
2363  get_value(AV self, StringKey a0) -> IMP::String
2364  get_value(AV self, ParticleIndexKey a0) -> Particle
2365  get_value(AV self, ObjectKey a0) -> Object
2366  get_value(AV self, SparseFloatKey a0) -> IMP::Float
2367  get_value(AV self, SparseIntKey a0) -> IMP::Int
2368  get_value(AV self, SparseStringKey a0) -> IMP::String
2369  get_value(AV self, SparseParticleIndexKey a0) -> ParticleIndex
2370  """
2371  return _IMP_bff.AV_get_value(self, *args)
2372 
2373  def set_value(self, *args):
2374  r"""
2375  set_value(AV self, FloatKey a0, IMP::Float a1)
2376  set_value(AV self, IntKey a0, IMP::Int a1)
2377  set_value(AV self, FloatsKey a0, IMP::Floats a1)
2378  set_value(AV self, IntsKey a0, IMP::Ints a1)
2379  set_value(AV self, StringKey a0, IMP::String a1)
2380  set_value(AV self, ParticleIndexKey a0, Particle a1)
2381  set_value(AV self, ObjectKey a0, Object a1)
2382  set_value(AV self, SparseFloatKey a0, IMP::Float a1)
2383  set_value(AV self, SparseIntKey a0, IMP::Int a1)
2384  set_value(AV self, SparseStringKey a0, IMP::String a1)
2385  set_value(AV self, SparseParticleIndexKey a0, ParticleIndex a1)
2386  """
2387  return _IMP_bff.AV_set_value(self, *args)
2388 
2389  def remove_attribute(self, *args):
2390  r"""
2391  remove_attribute(AV self, FloatKey a0)
2392  remove_attribute(AV self, IntKey a0)
2393  remove_attribute(AV self, FloatsKey a0)
2394  remove_attribute(AV self, IntsKey a0)
2395  remove_attribute(AV self, StringKey a0)
2396  remove_attribute(AV self, ParticleIndexKey a0)
2397  remove_attribute(AV self, ObjectKey a0)
2398  remove_attribute(AV self, SparseFloatKey a0)
2399  remove_attribute(AV self, SparseIntKey a0)
2400  remove_attribute(AV self, SparseStringKey a0)
2401  remove_attribute(AV self, SparseParticleIndexKey a0)
2402  """
2403  return _IMP_bff.AV_remove_attribute(self, *args)
2404 
2405  def has_attribute(self, *args):
2406  r"""
2407  has_attribute(AV self, FloatKey a0) -> bool
2408  has_attribute(AV self, IntKey a0) -> bool
2409  has_attribute(AV self, FloatsKey a0) -> bool
2410  has_attribute(AV self, IntsKey a0) -> bool
2411  has_attribute(AV self, StringKey a0) -> bool
2412  has_attribute(AV self, ParticleIndexKey a0) -> bool
2413  has_attribute(AV self, ObjectKey a0) -> bool
2414  has_attribute(AV self, SparseFloatKey a0) -> bool
2415  has_attribute(AV self, SparseIntKey a0) -> bool
2416  has_attribute(AV self, SparseStringKey a0) -> bool
2417  has_attribute(AV self, SparseParticleIndexKey a0) -> bool
2418  """
2419  return _IMP_bff.AV_has_attribute(self, *args)
2420 
2421  def get_derivative(self, a0):
2422  r"""get_derivative(AV self, FloatKey a0) -> double"""
2423  return _IMP_bff.AV_get_derivative(self, a0)
2424 
2425  def get_name(self):
2426  r"""get_name(AV self) -> std::string"""
2427  return _IMP_bff.AV_get_name(self)
2428 
2429  def clear_caches(self):
2430  r"""clear_caches(AV self)"""
2431  return _IMP_bff.AV_clear_caches(self)
2432 
2433  def set_name(self, a0):
2434  r"""set_name(AV self, std::string a0)"""
2435  return _IMP_bff.AV_set_name(self, a0)
2436 
2437  def set_check_level(self, a0):
2438  r"""set_check_level(AV self, IMP::CheckLevel a0)"""
2439  return _IMP_bff.AV_set_check_level(self, a0)
2440 
2441  def add_to_derivative(self, a0, a1, a2):
2442  r"""add_to_derivative(AV self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2443  return _IMP_bff.AV_add_to_derivative(self, a0, a1, a2)
2444 
2445  def set_is_optimized(self, a0, a1):
2446  r"""set_is_optimized(AV self, FloatKey a0, bool a1)"""
2447  return _IMP_bff.AV_set_is_optimized(self, a0, a1)
2448 
2449  def get_is_optimized(self, a0):
2450  r"""get_is_optimized(AV self, FloatKey a0) -> bool"""
2451  return _IMP_bff.AV_get_is_optimized(self, a0)
2452 
2453  def get_check_level(self):
2454  r"""get_check_level(AV self) -> IMP::CheckLevel"""
2455  return _IMP_bff.AV_get_check_level(self)
2456 
2457  def __eq__(self, *args):
2458  r"""
2459  __eq__(AV self, AV o) -> bool
2460  __eq__(AV self, Particle d) -> bool
2461  """
2462  return _IMP_bff.AV___eq__(self, *args)
2463 
2464  def __ne__(self, *args):
2465  r"""
2466  __ne__(AV self, AV o) -> bool
2467  __ne__(AV self, Particle d) -> bool
2468  """
2469  return _IMP_bff.AV___ne__(self, *args)
2470 
2471  def __le__(self, *args):
2472  r"""
2473  __le__(AV self, AV o) -> bool
2474  __le__(AV self, Particle d) -> bool
2475  """
2476  return _IMP_bff.AV___le__(self, *args)
2477 
2478  def __lt__(self, *args):
2479  r"""
2480  __lt__(AV self, AV o) -> bool
2481  __lt__(AV self, Particle d) -> bool
2482  """
2483  return _IMP_bff.AV___lt__(self, *args)
2484 
2485  def __ge__(self, *args):
2486  r"""
2487  __ge__(AV self, AV o) -> bool
2488  __ge__(AV self, Particle d) -> bool
2489  """
2490  return _IMP_bff.AV___ge__(self, *args)
2491 
2492  def __gt__(self, *args):
2493  r"""
2494  __gt__(AV self, AV o) -> bool
2495  __gt__(AV self, Particle d) -> bool
2496  """
2497  return _IMP_bff.AV___gt__(self, *args)
2498 
2499  def __hash__(self):
2500  r"""__hash__(AV self) -> std::size_t"""
2501  return _IMP_bff.AV___hash__(self)
2502 
2503  def __str__(self):
2504  r"""__str__(AV self) -> std::string"""
2505  return _IMP_bff.AV___str__(self)
2506 
2507  def __repr__(self):
2508  r"""__repr__(AV self) -> std::string"""
2509  return _IMP_bff.AV___repr__(self)
2510 
2511  def _get_as_binary(self):
2512  r"""_get_as_binary(AV self) -> PyObject *"""
2513  return _IMP_bff.AV__get_as_binary(self)
2514 
2515  def _set_from_binary(self, p):
2516  r"""_set_from_binary(AV self, PyObject * p)"""
2517  return _IMP_bff.AV__set_from_binary(self, p)
2518 
2519  def __getstate__(self):
2520  p = self._get_as_binary()
2521  if len(self.__dict__) > 1:
2522  d = self.__dict__.copy()
2523  del d['this']
2524  p = (d, p)
2525  return p
2526 
2527  def __setstate__(self, p):
2528  if not hasattr(self, 'this'):
2529  self.__init__()
2530  if isinstance(p, tuple):
2531  d, p = p
2532  self.__dict__.update(d)
2533  return self._set_from_binary(p)
2534 
2535 
2536  map = property(get_map)
2537 
2538  __swig_destroy__ = _IMP_bff.delete_AV
2539 
2540 # Register AV in _IMP_bff:
2541 _IMP_bff.AV_swigregister(AV)
2542 
2543 def __lshift__(out, n):
2544  r"""__lshift__(_ostream out, AV n) -> _ostream"""
2545  return _IMP_bff.__lshift__(out, n)
2546 
2547 def av_distance(*args, **kwargs):
2548  r"""av_distance(AV a, AV b, double forster_radius=52.0, int distance_type=DYE_PAIR_DISTANCE_MEAN, int n_samples=10000) -> double"""
2549  return _IMP_bff.av_distance(*args, **kwargs)
2550 
2551 def av_random_points(av1, n_samples=10000):
2552  r"""av_random_points(AV av1, int n_samples=10000) -> VectorDouble"""
2553  return _IMP_bff.av_random_points(av1, n_samples)
2554 
2555 def av_random_distances(av1, av2, n_samples=10000):
2556  r"""av_random_distances(AV av1, AV av2, int n_samples=10000) -> VectorDouble"""
2557  return _IMP_bff.av_random_distances(av1, av2, n_samples)
2558 
2559 def av_distance_distribution(av1, av2, axis, n_samples=10000):
2560  r"""av_distance_distribution(AV av1, AV av2, VectorDouble axis, int n_samples=10000) -> VectorDouble"""
2561  return _IMP_bff.av_distance_distribution(av1, av2, axis, n_samples)
2562 
2563 def search_labeling_site(*args, **kwargs):
2564  r"""search_labeling_site(Hierarchy hier, std::string json_str="", nlohmann::json const & json_data=nlohmann::json()) -> ParticleIndex"""
2565  return _IMP_bff.search_labeling_site(*args, **kwargs)
2566 class AVNetworkRestraint(IMP.Restraint):
2567  r"""Proxy of C++ IMP::bff::AVNetworkRestraint class."""
2568 
2569  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2570 
2571  def __init__(self, *args, **kwargs):
2572  r"""__init__(AVNetworkRestraint self, Hierarchy hier, std::string fps_json_fn, std::string name="AVNetworkRestraint%1%", std::string score_set="", int n_samples=50000) -> AVNetworkRestraint"""
2573  _IMP_bff.AVNetworkRestraint_swiginit(self, _IMP_bff.new_AVNetworkRestraint(*args, **kwargs))
2574 
2575  def get_probability(self):
2576  r"""get_probability(AVNetworkRestraint self) -> double"""
2577  return _IMP_bff.AVNetworkRestraint_get_probability(self)
2578 
2579  def get_used_avs(self):
2580  r"""get_used_avs(AVNetworkRestraint self) -> IMP::bff::AVs const"""
2581  return _IMP_bff.AVNetworkRestraint_get_used_avs(self)
2582 
2583  def get_used_distances(self):
2584  r"""get_used_distances(AVNetworkRestraint self) -> MapStringAVPairDistanceMeasurement"""
2585  return _IMP_bff.AVNetworkRestraint_get_used_distances(self)
2586 
2587  def get_model_distance(self, position1_name, position2_name, forster_radius, distance_type):
2588  r"""get_model_distance(AVNetworkRestraint self, std::string position1_name, std::string position2_name, double forster_radius, int distance_type) -> double"""
2589  return _IMP_bff.AVNetworkRestraint_get_model_distance(self, position1_name, position2_name, forster_radius, distance_type)
2590 
2591  def get_indexes(self):
2592  r"""get_indexes(AVNetworkRestraint self) -> IMP::ParticleIndexes const"""
2593  return _IMP_bff.AVNetworkRestraint_get_indexes(self)
2594 
2595  def do_get_inputs(self):
2596  r"""do_get_inputs(AVNetworkRestraint self) -> IMP::ModelObjectsTemp"""
2597  return _IMP_bff.AVNetworkRestraint_do_get_inputs(self)
2598 
2599  def show(self, out):
2600  r"""show(AVNetworkRestraint self, _ostream out)"""
2601  return _IMP_bff.AVNetworkRestraint_show(self, out)
2602 
2603  def get_version_info(self):
2604  r"""get_version_info(AVNetworkRestraint self) -> VersionInfo"""
2605  return _IMP_bff.AVNetworkRestraint_get_version_info(self)
2606  __swig_destroy__ = _IMP_bff.delete_AVNetworkRestraint
2607 
2608  def __str__(self):
2609  r"""__str__(AVNetworkRestraint self) -> std::string"""
2610  return _IMP_bff.AVNetworkRestraint___str__(self)
2611 
2612  def __repr__(self):
2613  r"""__repr__(AVNetworkRestraint self) -> std::string"""
2614  return _IMP_bff.AVNetworkRestraint___repr__(self)
2615 
2616  @staticmethod
2617  def get_from(o):
2618  return _object_cast_to_AVNetworkRestraint(o)
2619 
2620 
2621 # Register AVNetworkRestraint in _IMP_bff:
2622 _IMP_bff.AVNetworkRestraint_swigregister(AVNetworkRestraint)
2623 
2624 def decay_rescale(fit, decay, start=0, stop=-1):
2625  r"""decay_rescale(double * fit, double * decay, int start=0, int stop=-1) -> double"""
2626  return _IMP_bff.decay_rescale(fit, decay, start, stop)
2627 
2628 def decay_rescale_w(fit, decay, w_sq, start=0, stop=-1):
2629  r"""decay_rescale_w(double * fit, double * decay, double * w_sq, int start=0, int stop=-1) -> double"""
2630  return _IMP_bff.decay_rescale_w(fit, decay, w_sq, start, stop)
2631 
2632 def decay_rescale_w_bg(fit, decay, w_sq, bg=0.0, start=0, stop=-1):
2633  r"""decay_rescale_w_bg(double * fit, double * decay, double * w_sq, double bg=0.0, int start=0, int stop=-1) -> double"""
2634  return _IMP_bff.decay_rescale_w_bg(fit, decay, w_sq, bg, start, stop)
2635 
2636 def decay_fconv(fit, irf, x, start=0, stop=-1, dt=1.0):
2637  r"""decay_fconv(double * fit, double * irf, double * x, int start=0, int stop=-1, double dt=1.0)"""
2638  return _IMP_bff.decay_fconv(fit, irf, x, start, stop, dt)
2639 
2640 def decay_fconv_avx(fit, irf, x, start=0, stop=-1, dt=1.0):
2641  r"""decay_fconv_avx(double * fit, double * irf, double * x, int start=0, int stop=-1, double dt=1.0)"""
2642  return _IMP_bff.decay_fconv_avx(fit, irf, x, start, stop, dt)
2643 
2644 def decay_fconv_per(fit, irf, x, period, start=0, stop=-1, dt=1.0):
2645  r"""decay_fconv_per(double * fit, double * irf, double * x, double period, int start=0, int stop=-1, double dt=1.0)"""
2646  return _IMP_bff.decay_fconv_per(fit, irf, x, period, start, stop, dt)
2647 
2648 def decay_fconv_per_avx(fit, irf, x, period, start=0, stop=-1, dt=1.0):
2649  r"""decay_fconv_per_avx(double * fit, double * irf, double * x, double period, int start=0, int stop=-1, double dt=1.0)"""
2650  return _IMP_bff.decay_fconv_per_avx(fit, irf, x, period, start, stop, dt)
2651 
2652 def decay_fconv_per_cs(fit, irf, x, period, conv_stop=-1, stop=-1, dt=1.0):
2653  r"""decay_fconv_per_cs(double * fit, double * irf, double * x, double period, int conv_stop=-1, int stop=-1, double dt=1.0)"""
2654  return _IMP_bff.decay_fconv_per_cs(fit, irf, x, period, conv_stop, stop, dt)
2655 
2656 def decay_fconv_ref(fit, irf, x, tauref, start=0, stop=-1, dt=1.0):
2657  r"""decay_fconv_ref(double * fit, double * irf, double * x, double tauref, int start=0, int stop=-1, double dt=1.0)"""
2658  return _IMP_bff.decay_fconv_ref(fit, irf, x, tauref, start, stop, dt)
2659 
2660 def decay_sconv(fit, irf, model, start=0, stop=-1):
2661  r"""decay_sconv(double * fit, double * irf, double * model, int start=0, int stop=-1)"""
2662  return _IMP_bff.decay_sconv(fit, irf, model, start, stop)
2663 
2664 def decay_shift_lamp(irf, irf_shift, ts):
2665  r"""decay_shift_lamp(double * irf, double * irf_shift, double ts)"""
2666  return _IMP_bff.decay_shift_lamp(irf, irf_shift, ts)
2667 
2668 def mod_p(a, n):
2669  r"""mod_p(int a, int n) -> int"""
2670  return _IMP_bff.mod_p(a, n)
2671 
2672 def decay_add_pile_up_to_model(*args, **kwargs):
2673  r"""decay_add_pile_up_to_model(double * model, double * data, double repetition_rate, double instrument_dead_time, double measurement_time, std::string pile_up_model="coates", int start=0, int stop=-1)"""
2674  return _IMP_bff.decay_add_pile_up_to_model(*args, **kwargs)
2675 
2676 def discriminate_small_amplitudes(lifetime_spectrum, amplitude_threshold):
2677  r"""discriminate_small_amplitudes(double * lifetime_spectrum, double amplitude_threshold)"""
2678  return _IMP_bff.discriminate_small_amplitudes(lifetime_spectrum, amplitude_threshold)
2679 
2680 def decay_fconv_per_cs_time_axis(model, time_axis, irf, lifetime_spectrum, convolution_start=0, convolution_stop=-1, period=100.0):
2681  r"""decay_fconv_per_cs_time_axis(double * model, double * time_axis, double * irf, double * lifetime_spectrum, int convolution_start=0, int convolution_stop=-1, double period=100.0)"""
2682  return _IMP_bff.decay_fconv_per_cs_time_axis(model, time_axis, irf, lifetime_spectrum, convolution_start, convolution_stop, period)
2683 
2684 def decay_fconv_cs_time_axis(inplace_output, time_axis, irf, lifetime_spectrum, convolution_start=0, convolution_stop=-1):
2685  r"""decay_fconv_cs_time_axis(double * inplace_output, double * time_axis, double * irf, double * lifetime_spectrum, int convolution_start=0, int convolution_stop=-1)"""
2686  return _IMP_bff.decay_fconv_cs_time_axis(inplace_output, time_axis, irf, lifetime_spectrum, convolution_start, convolution_stop)
2687 NOISE_NA = _IMP_bff.NOISE_NA
2688 
2689 NOISE_POISSON = _IMP_bff.NOISE_POISSON
2690 
2691 class DecayCurve(object):
2692  r"""Proxy of C++ IMP::bff::DecayCurve class."""
2693 
2694  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2695  __repr__ = _swig_repr
2696 
2697  @staticmethod
2698  def shift_array(input, shift):
2699  r"""shift_array(double * input, double shift) -> VectorDouble"""
2700  return _IMP_bff.DecayCurve_shift_array(input, shift)
2701 
2702  def size(self):
2703  r"""size(DecayCurve self) -> size_t"""
2704  return _IMP_bff.DecayCurve_size(self)
2705 
2706  def empty(self):
2707  r"""empty(DecayCurve self) -> bool"""
2708  return _IMP_bff.DecayCurve_empty(self)
2709 
2710  def get_dx(self):
2711  r"""get_dx(DecayCurve self) -> VectorDouble"""
2712  return _IMP_bff.DecayCurve_get_dx(self)
2713 
2714  def resize(self, n, v=0.0, dx=1.0):
2715  r"""resize(DecayCurve self, size_t n, double v=0.0, double dx=1.0)"""
2716  return _IMP_bff.DecayCurve_resize(self, n, v, dx)
2717 
2718  def get_average_dx(self):
2719  r"""get_average_dx(DecayCurve self) -> double"""
2720  return _IMP_bff.DecayCurve_get_average_dx(self)
2721 
2722  def get_x(self):
2723  r"""get_x(DecayCurve self) -> VectorDouble"""
2724  return _IMP_bff.DecayCurve_get_x(self)
2725 
2726  def set_x(self, *args):
2727  r"""
2728  set_x(DecayCurve self, VectorDouble v)
2729  set_x(DecayCurve self, double * input)
2730  """
2731  return _IMP_bff.DecayCurve_set_x(self, *args)
2732 
2733  def get_y(self):
2734  r"""get_y(DecayCurve self) -> VectorDouble"""
2735  return _IMP_bff.DecayCurve_get_y(self)
2736 
2737  def set_y(self, *args):
2738  r"""
2739  set_y(DecayCurve self, VectorDouble v)
2740  set_y(DecayCurve self, double * input)
2741  """
2742  return _IMP_bff.DecayCurve_set_y(self, *args)
2743 
2744  def get_ey(self):
2745  r"""get_ey(DecayCurve self) -> VectorDouble"""
2746  return _IMP_bff.DecayCurve_get_ey(self)
2747 
2748  def set_ey(self, *args):
2749  r"""
2750  set_ey(DecayCurve self, VectorDouble v)
2751  set_ey(DecayCurve self, double * input)
2752  """
2753  return _IMP_bff.DecayCurve_set_ey(self, *args)
2754 
2755  def set_acquisition_time(self, v):
2756  r"""set_acquisition_time(DecayCurve self, double v)"""
2757  return _IMP_bff.DecayCurve_set_acquisition_time(self, v)
2758 
2759  def get_acquisition_time(self):
2760  r"""get_acquisition_time(DecayCurve self) -> double"""
2761  return _IMP_bff.DecayCurve_get_acquisition_time(self)
2762 
2763  def set_shift(self, v):
2764  r"""set_shift(DecayCurve self, double v)"""
2765  return _IMP_bff.DecayCurve_set_shift(self, v)
2766 
2767  def get_shift(self):
2768  r"""get_shift(DecayCurve self) -> double"""
2769  return _IMP_bff.DecayCurve_get_shift(self)
2770 
2771  def get_json(self):
2772  r"""get_json(DecayCurve self) -> std::string"""
2773  return _IMP_bff.DecayCurve_get_json(self)
2774 
2775  def read_json(self, json_string):
2776  r"""read_json(DecayCurve self, std::string json_string) -> int"""
2777  return _IMP_bff.DecayCurve_read_json(self, json_string)
2778 
2779  def __init__(self, *args, **kwargs):
2780  r"""__init__(DecayCurve self, VectorDouble x=std::vector< double >(), VectorDouble y=std::vector< double >(), VectorDouble ey=std::vector< double >(), double acquisition_time=std::numeric_limits< double >::max(), int noise_model=NOISE_POISSON, int size=-1) -> DecayCurve"""
2781  _IMP_bff.DecayCurve_swiginit(self, _IMP_bff.new_DecayCurve(*args, **kwargs))
2782 
2783  def sum(self, start=0, stop=-1):
2784  r"""sum(DecayCurve self, int start=0, int stop=-1) -> double"""
2785  return _IMP_bff.DecayCurve_sum(self, start, stop)
2786 
2787  def apply_simple_moving_average(self, start, stop, n_window=5, normalize=False):
2788  r"""apply_simple_moving_average(DecayCurve self, int start, int stop, int n_window=5, bool normalize=False)"""
2789  return _IMP_bff.DecayCurve_apply_simple_moving_average(self, start, stop, n_window, normalize)
2790 
2791  def __iadd__(self, v):
2792  r"""__iadd__(DecayCurve self, double v) -> DecayCurve"""
2793  return _IMP_bff.DecayCurve___iadd__(self, v)
2794 
2795  def __isub__(self, v):
2796  r"""__isub__(DecayCurve self, double v) -> DecayCurve"""
2797  return _IMP_bff.DecayCurve___isub__(self, v)
2798 
2799  def __imul__(self, v):
2800  r"""__imul__(DecayCurve self, double v) -> DecayCurve"""
2801  return _IMP_bff.DecayCurve___imul__(self, v)
2802 
2803  def __itruediv__(self, *args):
2804  return _IMP_bff.DecayCurve___itruediv__(self, *args)
2805  __idiv__ = __itruediv__
2806 
2807 
2808 
2809  def __add__(self, *args):
2810  r"""
2811  __add__(DecayCurve self, double v) -> DecayCurve
2812  __add__(DecayCurve self, DecayCurve other) -> DecayCurve
2813  """
2814  return _IMP_bff.DecayCurve___add__(self, *args)
2815 
2816  def __sub__(self, *args):
2817  r"""
2818  __sub__(DecayCurve self, double v) -> DecayCurve
2819  __sub__(DecayCurve self, DecayCurve other) -> DecayCurve
2820  """
2821  return _IMP_bff.DecayCurve___sub__(self, *args)
2822 
2823  def __mul__(self, *args):
2824  r"""
2825  __mul__(DecayCurve self, double v) -> DecayCurve
2826  __mul__(DecayCurve self, DecayCurve other) -> DecayCurve
2827  """
2828  return _IMP_bff.DecayCurve___mul__(self, *args)
2829 
2830  def __truediv__(self, *args):
2831  return _IMP_bff.DecayCurve___truediv__(self, *args)
2832  __div__ = __truediv__
2833 
2834 
2835 
2836  def __lshift__(self, v):
2837  r"""__lshift__(DecayCurve self, double v) -> DecayCurve"""
2838  return _IMP_bff.DecayCurve___lshift__(self, v)
2839 
2840  acquisition_time = property(get_acquisition_time, set_acquisition_time)
2841 
2842 
2843  shift = property(get_shift, set_shift)
2844 
2845 
2846  x = property(
2847  lambda x: np.array(x.get_x()),
2848  set_x
2849  )
2850 
2851 
2852  y = property(
2853  lambda x: np.array(x.get_y()),
2854  set_y
2855  )
2856 
2857 
2858  ey = property(
2859  lambda x: np.array(x.get_ey()),
2860  set_ey
2861  )
2862 
2863  __swig_destroy__ = _IMP_bff.delete_DecayCurve
2864 
2865 # Register DecayCurve in _IMP_bff:
2866 _IMP_bff.DecayCurve_swigregister(DecayCurve)
2867 
2868 DecayRanges=list
2869 _plural_types.append("DecayRanges")
2870 _value_types.append("DecayRange")
2871 
2872 class DecayRange(IMP._Value):
2873  r"""Proxy of C++ IMP::bff::DecayRange class."""
2874 
2875  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2876 
2877  def get_start(self, d=None):
2878  r"""get_start(DecayRange self, DecayCurve d=None) -> size_t"""
2879  return _IMP_bff.DecayRange_get_start(self, d)
2880 
2881  def get_stop(self, d=None):
2882  r"""get_stop(DecayRange self, DecayCurve d=None) -> size_t"""
2883  return _IMP_bff.DecayRange_get_stop(self, d)
2884 
2885  def set_range(self, v):
2886  r"""set_range(DecayRange self, VectorInt v)"""
2887  return _IMP_bff.DecayRange_set_range(self, v)
2888 
2889  def get_range(self, d=None):
2890  r"""get_range(DecayRange self, DecayCurve d=None) -> VectorInt"""
2891  return _IMP_bff.DecayRange_get_range(self, d)
2892 
2893  def set(self, start=0, stop=-1):
2894  r"""set(DecayRange self, int start=0, int stop=-1)"""
2895  return _IMP_bff.DecayRange_set(self, start, stop)
2896 
2897  def __init__(self, start, stop):
2898  r"""__init__(DecayRange self, int start, int stop) -> DecayRange"""
2899  _IMP_bff.DecayRange_swiginit(self, _IMP_bff.new_DecayRange(start, stop))
2900  __swig_destroy__ = _IMP_bff.delete_DecayRange
2901 
2902  def show(self, *args, **kwargs):
2903  r"""show(DecayRange self, _ostream out=std::cout)"""
2904  return _IMP_bff.DecayRange_show(self, *args, **kwargs)
2905 
2906  def __str__(self):
2907  r"""__str__(DecayRange self) -> std::string"""
2908  return _IMP_bff.DecayRange___str__(self)
2909 
2910  def __repr__(self):
2911  r"""__repr__(DecayRange self) -> std::string"""
2912  return _IMP_bff.DecayRange___repr__(self)
2913  start = property(_IMP_bff.DecayRange_start_get, _IMP_bff.DecayRange_start_set, doc=r"""start : int""")
2914  stop = property(_IMP_bff.DecayRange_stop_get, _IMP_bff.DecayRange_stop_set, doc=r"""stop : int""")
2915 
2916 # Register DecayRange in _IMP_bff:
2917 _IMP_bff.DecayRange_swigregister(DecayRange)
2918 
2919 _object_types.append("DecayLifetimeHandler")
2920 
2921 
2922 def _object_cast_to_DecayLifetimeHandler(o):
2923  r"""_object_cast_to_DecayLifetimeHandler(Object o) -> DecayLifetimeHandler"""
2924  return _IMP_bff._object_cast_to_DecayLifetimeHandler(o)
2925 class DecayLifetimeHandler(IMP.Object):
2926  r"""Proxy of C++ IMP::bff::DecayLifetimeHandler class."""
2927 
2928  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2929 
2930  def add_lifetime(self, amplitude, lifetime):
2931  r"""add_lifetime(DecayLifetimeHandler self, double amplitude, double lifetime)"""
2932  return _IMP_bff.DecayLifetimeHandler_add_lifetime(self, amplitude, lifetime)
2933 
2934  def get_lifetime_spectrum(self):
2935  r"""get_lifetime_spectrum(DecayLifetimeHandler self)"""
2936  return _IMP_bff.DecayLifetimeHandler_get_lifetime_spectrum(self)
2937 
2938  def __init__(self, *args, **kwargs):
2939  r"""__init__(DecayLifetimeHandler self, VectorDouble lifetime_spectrum=std::vector< double >(), bool use_amplitude_threshold=False, bool abs_lifetime_spectrum=False, double amplitude_threshold=std::numeric_limits< double >::epsilon()) -> DecayLifetimeHandler"""
2940  _IMP_bff.DecayLifetimeHandler_swiginit(self, _IMP_bff.new_DecayLifetimeHandler(*args, **kwargs))
2941 
2942  def get_version_info(self):
2943  r"""get_version_info(DecayLifetimeHandler self) -> VersionInfo"""
2944  return _IMP_bff.DecayLifetimeHandler_get_version_info(self)
2945  __swig_destroy__ = _IMP_bff.delete_DecayLifetimeHandler
2946 
2947  def __str__(self):
2948  r"""__str__(DecayLifetimeHandler self) -> std::string"""
2949  return _IMP_bff.DecayLifetimeHandler___str__(self)
2950 
2951  def __repr__(self):
2952  r"""__repr__(DecayLifetimeHandler self) -> std::string"""
2953  return _IMP_bff.DecayLifetimeHandler___repr__(self)
2954 
2955  @staticmethod
2956  def get_from(o):
2957  return _object_cast_to_DecayLifetimeHandler(o)
2958 
2959  abs_lifetime_spectrum = property(_IMP_bff.DecayLifetimeHandler_abs_lifetime_spectrum_get, _IMP_bff.DecayLifetimeHandler_abs_lifetime_spectrum_set, doc=r"""abs_lifetime_spectrum : bool""")
2960  use_amplitude_threshold = property(_IMP_bff.DecayLifetimeHandler_use_amplitude_threshold_get, _IMP_bff.DecayLifetimeHandler_use_amplitude_threshold_set, doc=r"""use_amplitude_threshold : bool""")
2961  amplitude_threshold = property(_IMP_bff.DecayLifetimeHandler_amplitude_threshold_get, _IMP_bff.DecayLifetimeHandler_amplitude_threshold_set, doc=r"""amplitude_threshold : double""")
2962  lifetime_spectrum = property(_IMP_bff.DecayLifetimeHandler_lifetime_spectrum_get, _IMP_bff.DecayLifetimeHandler_lifetime_spectrum_set, doc=r"""lifetime_spectrum : std::vector<(double,std::allocator<(double)>)>""")
2963 
2964 # Register DecayLifetimeHandler in _IMP_bff:
2965 _IMP_bff.DecayLifetimeHandler_swigregister(DecayLifetimeHandler)
2966 
2967 DecayModifiers=list
2968 _plural_types.append("DecayModifiers")
2969 _value_types.append("DecayModifier")
2970 
2971 class DecayModifier(DecayRange):
2972  r"""Proxy of C++ IMP::bff::DecayModifier class."""
2973 
2974  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2975 
2976  def __init__(self, *args, **kwargs):
2977  raise AttributeError("No constructor defined - class is abstract")
2978 
2979  def set_data(self, v):
2980  r"""set_data(DecayModifier self, DecayCurve v)"""
2981  return _IMP_bff.DecayModifier_set_data(self, v)
2982 
2983  def get_data(self):
2984  r"""get_data(DecayModifier self) -> DecayCurve"""
2985  return _IMP_bff.DecayModifier_get_data(self)
2986 
2987  def set(self, data, start=0, stop=-1, active=True):
2988  r"""set(DecayModifier self, DecayCurve data, int start=0, int stop=-1, bool active=True)"""
2989  return _IMP_bff.DecayModifier_set(self, data, start, stop, active)
2990 
2991  def resize(self, n, v=0.0):
2992  r"""resize(DecayModifier self, size_t n, double v=0.0)"""
2993  return _IMP_bff.DecayModifier_resize(self, n, v)
2994 
2995  def add(self, out):
2996  r"""add(DecayModifier self, DecayCurve out)"""
2997  return _IMP_bff.DecayModifier_add(self, out)
2998  __swig_destroy__ = _IMP_bff.delete_DecayModifier
2999 
3000  def __str__(self):
3001  r"""__str__(DecayModifier self) -> std::string"""
3002  return _IMP_bff.DecayModifier___str__(self)
3003 
3004  def __repr__(self):
3005  r"""__repr__(DecayModifier self) -> std::string"""
3006  return _IMP_bff.DecayModifier___repr__(self)
3007  active = property(_IMP_bff.DecayModifier_active_get, _IMP_bff.DecayModifier_active_set, doc=r"""active : bool""")
3008 
3009  data = property(get_data, set_data)
3010 
3011 
3012  def __call__(self, *args, **kwargs):
3013  self.add(*args, **kwargs)
3014 
3015 
3016 # Register DecayModifier in _IMP_bff:
3017 _IMP_bff.DecayModifier_swigregister(DecayModifier)
3018 
3019 DecayConvolutions=list
3020 _plural_types.append("DecayConvolutions")
3021 _value_types.append("DecayConvolution")
3022 
3023 class DecayConvolution(DecayModifier):
3024  r"""Proxy of C++ IMP::bff::DecayConvolution class."""
3025 
3026  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3027  FAST_PERIODIC_TIME = _IMP_bff.DecayConvolution_FAST_PERIODIC_TIME
3028 
3029  FAST_TIME = _IMP_bff.DecayConvolution_FAST_TIME
3030 
3031  FAST_PERIODIC = _IMP_bff.DecayConvolution_FAST_PERIODIC
3032 
3033  FAST = _IMP_bff.DecayConvolution_FAST
3034 
3035  FAST_AVX = _IMP_bff.DecayConvolution_FAST_AVX
3036 
3037  FAST_PERIODIC_AVX = _IMP_bff.DecayConvolution_FAST_PERIODIC_AVX
3038 
3039 
3040  @staticmethod
3041  def compute_corrected_irf(irf, corrected_irf, irf_shift_channels, irf_background_counts):
3042  r"""compute_corrected_irf(DecayCurve irf, DecayCurve corrected_irf, double irf_shift_channels, double irf_background_counts)"""
3043  return _IMP_bff.DecayConvolution_compute_corrected_irf(irf, corrected_irf, irf_shift_channels, irf_background_counts)
3044 
3045  @staticmethod
3046  def compute_mean_lifetime(irf_histogram, decay_histogram, micro_time_resolution):
3047  r"""compute_mean_lifetime(VectorDouble irf_histogram, VectorDouble decay_histogram, double micro_time_resolution) -> double"""
3048  return _IMP_bff.DecayConvolution_compute_mean_lifetime(irf_histogram, decay_histogram, micro_time_resolution)
3049 
3050  def set_irf(self, v):
3051  r"""set_irf(DecayConvolution self, DecayCurve v)"""
3052  return _IMP_bff.DecayConvolution_set_irf(self, v)
3053 
3054  def get_irf(self):
3055  r"""get_irf(DecayConvolution self) -> DecayCurve"""
3056  return _IMP_bff.DecayConvolution_get_irf(self)
3057 
3058  def get_mean_lifetime(self, decay):
3059  r"""get_mean_lifetime(DecayConvolution self, DecayCurve decay) -> double"""
3060  return _IMP_bff.DecayConvolution_get_mean_lifetime(self, decay)
3061 
3062  def set(self, *args, **kwargs):
3063  r"""set(DecayConvolution self, int convolution_method=FAST_PERIODIC_TIME, double excitation_period=100, double irf_shift_channels=0.0, double irf_background_counts=0)"""
3064  return _IMP_bff.DecayConvolution_set(self, *args, **kwargs)
3065 
3066  def __init__(self, *args, **kwargs):
3067  r"""__init__(DecayConvolution self, DecayLifetimeHandler lifetime_handler=None, DecayCurve instrument_response_function=None, int convolution_method=FAST, double excitation_period=100, double irf_shift_channels=0.0, double irf_background_counts=0, int start=0, int stop=-1, bool active=True) -> DecayConvolution"""
3068  _IMP_bff.DecayConvolution_swiginit(self, _IMP_bff.new_DecayConvolution(*args, **kwargs))
3069  __swig_destroy__ = _IMP_bff.delete_DecayConvolution
3070 
3071  def __str__(self):
3072  r"""__str__(DecayConvolution self) -> std::string"""
3073  return _IMP_bff.DecayConvolution___str__(self)
3074 
3075  def __repr__(self):
3076  r"""__repr__(DecayConvolution self) -> std::string"""
3077  return _IMP_bff.DecayConvolution___repr__(self)
3078  corrected_irf = property(_IMP_bff.DecayConvolution_corrected_irf_get, doc=r"""corrected_irf : r.IMP::bff::DecayCurve""")
3079  convolution_method = property(_IMP_bff.DecayConvolution_convolution_method_get, _IMP_bff.DecayConvolution_convolution_method_set, doc=r"""convolution_method : int""")
3080  excitation_period = property(_IMP_bff.DecayConvolution_excitation_period_get, _IMP_bff.DecayConvolution_excitation_period_set, doc=r"""excitation_period : double""")
3081  irf_shift_channels = property(_IMP_bff.DecayConvolution_irf_shift_channels_get, _IMP_bff.DecayConvolution_irf_shift_channels_set, doc=r"""irf_shift_channels : double""")
3082  irf_background_counts = property(_IMP_bff.DecayConvolution_irf_background_counts_get, _IMP_bff.DecayConvolution_irf_background_counts_set, doc=r"""irf_background_counts : double""")
3083 
3084  irf = property(get_irf, set_irf)
3085 
3086 
3087 # Register DecayConvolution in _IMP_bff:
3088 _IMP_bff.DecayConvolution_swigregister(DecayConvolution)
3089 
3090 DecayPatterns=list
3091 _plural_types.append("DecayPatterns")
3092 _value_types.append("DecayPattern")
3093 
3094 class DecayPattern(DecayModifier):
3095  r"""Proxy of C++ IMP::bff::DecayPattern class."""
3096 
3097  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3098 
3099  def __init__(self, constant_offset=0.0, pattern=None, pattern_fraction=0.0, start=0, stop=-1, active=True):
3100  r"""__init__(DecayPattern self, double constant_offset=0.0, DecayCurve pattern=None, double pattern_fraction=0.0, int start=0, int stop=-1, bool active=True) -> DecayPattern"""
3101  _IMP_bff.DecayPattern_swiginit(self, _IMP_bff.new_DecayPattern(constant_offset, pattern, pattern_fraction, start, stop, active))
3102 
3103  def __str__(self):
3104  r"""__str__(DecayPattern self) -> std::string"""
3105  return _IMP_bff.DecayPattern___str__(self)
3106 
3107  def __repr__(self):
3108  r"""__repr__(DecayPattern self) -> std::string"""
3109  return _IMP_bff.DecayPattern___repr__(self)
3110  pattern = property(_IMP_bff.DecayPattern_pattern_get, _IMP_bff.DecayPattern_pattern_set, doc=r"""pattern : p.IMP::bff::DecayCurve""")
3111  pattern_fraction = property(_IMP_bff.DecayPattern_pattern_fraction_get, _IMP_bff.DecayPattern_pattern_fraction_set, doc=r"""pattern_fraction : double""")
3112  constant_offset = property(_IMP_bff.DecayPattern_constant_offset_get, _IMP_bff.DecayPattern_constant_offset_set, doc=r"""constant_offset : double""")
3113  __swig_destroy__ = _IMP_bff.delete_DecayPattern
3114 
3115 # Register DecayPattern in _IMP_bff:
3116 _IMP_bff.DecayPattern_swigregister(DecayPattern)
3117 
3118 DecayPileups=list
3119 _plural_types.append("DecayPileups")
3120 _value_types.append("DecayPileup")
3121 
3122 class DecayPileup(DecayModifier):
3123  r"""Proxy of C++ IMP::bff::DecayPileup class."""
3124 
3125  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3126 
3127  def __init__(self, *args, **kwargs):
3128  r"""__init__(DecayPileup self, DecayCurve data, char const * pile_up_model="coates", double repetition_rate=100, double instrument_dead_time=120, int start=0, int stop=-1, bool active=True) -> DecayPileup"""
3129  _IMP_bff.DecayPileup_swiginit(self, _IMP_bff.new_DecayPileup(*args, **kwargs))
3130 
3131  def __str__(self):
3132  r"""__str__(DecayPileup self) -> std::string"""
3133  return _IMP_bff.DecayPileup___str__(self)
3134 
3135  def __repr__(self):
3136  r"""__repr__(DecayPileup self) -> std::string"""
3137  return _IMP_bff.DecayPileup___repr__(self)
3138  instrument_dead_time = property(_IMP_bff.DecayPileup_instrument_dead_time_get, _IMP_bff.DecayPileup_instrument_dead_time_set, doc=r"""instrument_dead_time : double""")
3139  repetition_rate = property(_IMP_bff.DecayPileup_repetition_rate_get, _IMP_bff.DecayPileup_repetition_rate_set, doc=r"""repetition_rate : double""")
3140  pile_up_model = property(_IMP_bff.DecayPileup_pile_up_model_get, _IMP_bff.DecayPileup_pile_up_model_set, doc=r"""pile_up_model : std::string""")
3141  __swig_destroy__ = _IMP_bff.delete_DecayPileup
3142 
3143 # Register DecayPileup in _IMP_bff:
3144 _IMP_bff.DecayPileup_swigregister(DecayPileup)
3145 
3146 DecayLinearizations=list
3147 _plural_types.append("DecayLinearizations")
3148 _value_types.append("DecayLinearization")
3149 
3150 class DecayLinearization(DecayModifier):
3151  r"""Proxy of C++ IMP::bff::DecayLinearization class."""
3152 
3153  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3154 
3155  def set_linearization_table(self, v):
3156  r"""set_linearization_table(DecayLinearization self, DecayCurve v)"""
3157  return _IMP_bff.DecayLinearization_set_linearization_table(self, v)
3158 
3159  def get_linearization_table(self):
3160  r"""get_linearization_table(DecayLinearization self) -> DecayCurve"""
3161  return _IMP_bff.DecayLinearization_get_linearization_table(self)
3162 
3163  def __init__(self, linearization_table, start, stop, active=True, n_window=5):
3164  r"""__init__(DecayLinearization self, DecayCurve linearization_table, int start, int stop, bool active=True, int n_window=5) -> DecayLinearization"""
3165  _IMP_bff.DecayLinearization_swiginit(self, _IMP_bff.new_DecayLinearization(linearization_table, start, stop, active, n_window))
3166 
3167  def __str__(self):
3168  r"""__str__(DecayLinearization self) -> std::string"""
3169  return _IMP_bff.DecayLinearization___str__(self)
3170 
3171  def __repr__(self):
3172  r"""__repr__(DecayLinearization self) -> std::string"""
3173  return _IMP_bff.DecayLinearization___repr__(self)
3174  __swig_destroy__ = _IMP_bff.delete_DecayLinearization
3175 
3176 # Register DecayLinearization in _IMP_bff:
3177 _IMP_bff.DecayLinearization_swigregister(DecayLinearization)
3178 
3179 DecayScales=list
3180 _plural_types.append("DecayScales")
3181 _value_types.append("DecayScale")
3182 
3183 class DecayScale(DecayModifier):
3184  r"""Proxy of C++ IMP::bff::DecayScale class."""
3185 
3186  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3187 
3188  def set_blank_outside(self, v):
3189  r"""set_blank_outside(DecayScale self, double v)"""
3190  return _IMP_bff.DecayScale_set_blank_outside(self, v)
3191 
3192  def get_blank_outside(self):
3193  r"""get_blank_outside(DecayScale self) -> bool"""
3194  return _IMP_bff.DecayScale_get_blank_outside(self)
3195 
3196  def set(self, data=None, constant_background=0.0, start=0, stop=-1, active=True, blank_outside=True):
3197  r"""set(DecayScale self, DecayCurve data=None, double constant_background=0.0, int start=0, int stop=-1, bool active=True, bool blank_outside=True)"""
3198  return _IMP_bff.DecayScale_set(self, data, constant_background, start, stop, active, blank_outside)
3199 
3200  def __init__(self, data=None, constant_background=0.0, start=0, stop=-1, active=True, blank_outside=True):
3201  r"""__init__(DecayScale self, DecayCurve data=None, double constant_background=0.0, int start=0, int stop=-1, bool active=True, bool blank_outside=True) -> DecayScale"""
3202  _IMP_bff.DecayScale_swiginit(self, _IMP_bff.new_DecayScale(data, constant_background, start, stop, active, blank_outside))
3203 
3204  def __str__(self):
3205  r"""__str__(DecayScale self) -> std::string"""
3206  return _IMP_bff.DecayScale___str__(self)
3207 
3208  def __repr__(self):
3209  r"""__repr__(DecayScale self) -> std::string"""
3210  return _IMP_bff.DecayScale___repr__(self)
3211  number_of_photons = property(_IMP_bff.DecayScale_number_of_photons_get, doc=r"""number_of_photons : double""")
3212  constant_background = property(_IMP_bff.DecayScale_constant_background_get, _IMP_bff.DecayScale_constant_background_set, doc=r"""constant_background : double""")
3213  __swig_destroy__ = _IMP_bff.delete_DecayScale
3214 
3215 # Register DecayScale in _IMP_bff:
3216 _IMP_bff.DecayScale_swigregister(DecayScale)
3217 
3218 DecayScores=list
3219 _plural_types.append("DecayScores")
3220 _value_types.append("DecayScore")
3221 
3222 class DecayScore(DecayRange):
3223  r"""Proxy of C++ IMP::bff::DecayScore class."""
3224 
3225  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3226 
3227  def get_model(self):
3228  r"""get_model(DecayScore self) -> DecayCurve"""
3229  return _IMP_bff.DecayScore_get_model(self)
3230 
3231  def set_model(self, v):
3232  r"""set_model(DecayScore self, DecayCurve v)"""
3233  return _IMP_bff.DecayScore_set_model(self, v)
3234 
3235  def get_data(self):
3236  r"""get_data(DecayScore self) -> DecayCurve"""
3237  return _IMP_bff.DecayScore_get_data(self)
3238 
3239  def set_data(self, v):
3240  r"""set_data(DecayScore self, DecayCurve v)"""
3241  return _IMP_bff.DecayScore_set_data(self, v)
3242 
3243  def get_weighted_residuals(self):
3244  r"""get_weighted_residuals(DecayScore self) -> VectorDouble"""
3245  return _IMP_bff.DecayScore_get_weighted_residuals(self)
3246 
3247  def get_score(self, start=0, stop=-1, score_type=None):
3248  r"""get_score(DecayScore self, int start=0, int stop=-1, char const * score_type=None) -> double"""
3249  return _IMP_bff.DecayScore_get_score(self, start, stop, score_type)
3250 
3251  def set(self, *args, **kwargs):
3252  r"""set(DecayScore self, DecayCurve model, DecayCurve data, std::string score_type="poisson", int start=0, int stop=-1)"""
3253  return _IMP_bff.DecayScore_set(self, *args, **kwargs)
3254 
3255  def __init__(self, *args, **kwargs):
3256  r"""__init__(DecayScore self, DecayCurve model=None, DecayCurve data=None, std::string score_type="poisson", int start=0, int stop=-1) -> DecayScore"""
3257  _IMP_bff.DecayScore_swiginit(self, _IMP_bff.new_DecayScore(*args, **kwargs))
3258  __swig_destroy__ = _IMP_bff.delete_DecayScore
3259 
3260  def __str__(self):
3261  r"""__str__(DecayScore self) -> std::string"""
3262  return _IMP_bff.DecayScore___str__(self)
3263 
3264  def __repr__(self):
3265  r"""__repr__(DecayScore self) -> std::string"""
3266  return _IMP_bff.DecayScore___repr__(self)
3267  score_type = property(_IMP_bff.DecayScore_score_type_get, _IMP_bff.DecayScore_score_type_set, doc=r"""score_type : std::string""")
3268  score = property(_IMP_bff.DecayScore_score_get, doc=r"""score : double""")
3269 
3270  model = property(get_model, set_model)
3271 
3272 
3273  data = property(get_data, set_data)
3274 
3275 
3276  weighted_residuals = property(
3277  lambda x: np.array(x.get_weighted_residuals())
3278  )
3279 
3280 
3281 # Register DecayScore in _IMP_bff:
3282 _IMP_bff.DecayScore_swigregister(DecayScore)
3283 
3284 def get_module_name():
3285  r"""get_module_name() -> std::string const"""
3286  return _IMP_bff.get_module_name()
3287 
3288 def get_module_version():
3289  r"""get_module_version() -> std::string const"""
3290  return _IMP_bff.get_module_version()
3291 
3292 def get_example_path(fname):
3293  r"""get_example_path(std::string fname) -> std::string"""
3294  return _IMP_bff.get_example_path(fname)
3295 
3296 def get_data_path(fname):
3297  r"""get_data_path(std::string fname) -> std::string"""
3298  return _IMP_bff.get_data_path(fname)
3299 
3300 from . import _version_check
3301 _version_check.check_version(get_module_version())
3302 __version__ = get_module_version()
3303 
3304 
void decay_fconv_per_cs(double *fit, double *x, double *lamp, int numexp, int stop, int n_points, double period, int conv_stop, double dt)
Convolve lifetime spectrum - fast convolution, high repetition rate, with convolution stop...
void decay_fconv_avx(double *fit, double *x, double *lamp, int numexp, int start, int stop, double dt=0.05)
Convolve lifetime spectrum with instrument response (fast convolution, AVX optimized for large lifeti...
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:80
void decay_rescale_w_bg(double *fit, double *decay, double *e_sq, double bg, double *scale, int start, int stop)
Scale model function to the data (with weights and background)
Various classes to hold sets of particles.
void decay_fconv_cs_time_axis(double *inplace_output, int n_output, double *time_axis, int n_time_axis, double *irf, int n_irf, double *lifetime_spectrum, int n_lifetime_spectrum, int convolution_start=0, int convolution_stop=-1)
Make CGAL functionality available to IMP.
void decay_rescale_w(double *fit, double *decay, double *w_sq, double *scale, int start, int stop)
Scale model function to the data (with weights).
void decay_add_pile_up_to_model(double *model, int n_model, double *data, int n_data, double repetition_rate, double instrument_dead_time, double measurement_time, std::string pile_up_model="coates", int start=0, int stop=-1)
Add a pile-up distortion to the model function.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Composable functors to implement scores via compile-time composition.
double av_distance(const AV &a, const AV &b, double forster_radius=52.0, int distance_type=DYE_PAIR_DISTANCE_MEAN, int n_samples=10000)
Computes the distance to another accessible volume.
void decay_rescale(double *fit, double *decay, double *scale, int start, int stop)
Scale model function to the data (old version).
void decay_fconv(double *fit, double *x, double *lamp, int numexp, int start, int stop, double dt=0.05)
Convolve lifetime spectrum with instrument response (fast convolution, low repetition rate) ...
void decay_fconv_per(double *fit, double *x, double *lamp, int numexp, int start, int stop, int n_points, double period, double dt=0.05)
Convolve lifetime spectrum with instrument response (fast convolution, high repetition rate) ...
void decay_shift_lamp(double *lampsh, double *lamp, double ts, int n_points, double out_value=0.0)
shift instrument response function
Code to compute statistical measures.
std::vector< double > av_distance_distribution(const AV &av1, const AV &av2, std::vector< double > axis, int n_samples=10000)
Compute the distance to another accessible volume.
Class for sampling a density map from particles.
Common base class for heavy weight IMP objects.
Definition: Object.h:111
void decay_sconv(double *fit, double *p, double *lamp, int start, int stop)
Convolve fluorescence decay curve with irf.
Basic utilities for handling cryo-electron microscopy 3D density maps.
void decay_fconv_per_cs_time_axis(double *model, int n_model, double *time_axis, int n_time_axis, double *irf, int n_irf, double *lifetime_spectrum, int n_lifetime_spectrum, int convolution_start=0, int convolution_stop=-1, double period=100.0)
void decay_fconv_ref(double *fit, double *x, double *lamp, int numexp, int start, int stop, double tauref, double dt=0.05)
Convolve lifetime spectrum - fast convolution with reference compound decay.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
void write_path_map(PathMap *m, std::string filename, int value_type, const std::pair< float, float > bounds=std::pair< float, float >(std::numeric_limits< float >::min(), std::numeric_limits< float >::max()), const std::string &feature_name="")
Writes a path map to a file.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
void decay_fconv_per_avx(double *fit, double *x, double *lamp, int numexp, int start, int stop, int n_points, double period, double dt=0.05)
Convolve lifetime spectrum with instrument response (fast convolution, high repetition rate)...
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
void discriminate_small_amplitudes(double *lifetime_spectrum, int n_lifetime_spectrum, double amplitude_threshold)
std::vector< double > av_random_distances(const AV &av1, const AV &av2, int n_samples=10000)
Random sampling over AV/AV distances.
IMP::ParticleIndex search_labeling_site(const IMP::core::Hierarchy &hier, std::string json_str="", const nlohmann::json &json_data=nlohmann::json())
Find the particle index of a labeling site.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
ParticleIndexes get_indexes(const ParticlesTemp &ps)
Get the indexes from a list of particles.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:72
std::string get_module_version()
Return the version of this module, as a string.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:56
int mod_p(int a, int n)
Compute the modulo of a number with respect to a positive integer.
Definition: DecayRoutines.h:48